HEADER TRANSFERASE 18-DEC-14 4XD1 TITLE X-RAY STRUCTURE OF THE N-FORMYLTRANSFERASE QDTF FROM PROVIDENCIA TITLE 2 ALCALIFACIENS, W305A MUTANT, IN THE PRESENCE OF TDP-QUI3N AND N5-THF COMPND MOL_ID: 1; COMPND 2 MOLECULE: TDP-3-AMINOQUINOVOSE-N-FORMYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.2.9; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROVIDENCIA ALCALIFACIENS; SOURCE 3 ORGANISM_TAXID: 126385; SOURCE 4 GENE: QDTF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJ411 KEYWDS FORMYLTRANSFERASE, ANKYRIN REPEAT, LIPOPOLYSACCHARIDE, DEOXY SUGAR, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.B.THODEN,C.R.WOODFORD,H.M.HOLDEN REVDAT 4 27-SEP-23 4XD1 1 SOURCE JRNL REMARK LINK REVDAT 3 11-FEB-15 4XD1 1 JRNL REVDAT 2 04-FEB-15 4XD1 1 JRNL REVDAT 1 21-JAN-15 4XD1 0 JRNL AUTH C.R.WOODFORD,J.B.THODEN,H.M.HOLDEN JRNL TITL NEW ROLE FOR THE ANKYRIN REPEAT REVEALED BY A STUDY OF THE JRNL TITL 2 N-FORMYLTRANSFERASE FROM PROVIDENCIA ALCALIFACIENS. JRNL REF BIOCHEMISTRY V. 54 631 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 25574689 JRNL DOI 10.1021/BI501539A REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 69887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3695 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4754 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 247 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 605 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -1.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.606 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3437 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3282 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4659 ; 2.084 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7580 ; 0.932 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 412 ; 6.479 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;37.080 ;25.438 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 619 ;12.942 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;14.143 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 521 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3824 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 785 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4XD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73582 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4XCZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5-7% PEG 8000, 100 MM HEPPS, 200 MM REMARK 280 NACL, 200 MM KCL, 5 MM TDP, 5 MM N5-THF, PH 8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.55250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.13950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.13950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.77625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.13950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.13950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.32875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.13950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.13950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.77625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.13950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.13950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.32875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.55250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 78.27900 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 78.27900 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.55250 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 553 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 593 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 657 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 701 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 335 O HOH A 1041 1.80 REMARK 500 O HOH A 622 O HOH A 656 1.83 REMARK 500 O HOH A 641 O HOH A 656 1.94 REMARK 500 O HOH A 800 O HOH A 1003 1.94 REMARK 500 O HOH A 801 O HOH A 1002 1.97 REMARK 500 O3A T3Q A 402 O HOH A 905 1.98 REMARK 500 OE2 FON A 401 O HOH A 501 1.99 REMARK 500 OD1 ASP A 126 O HOH A 502 2.04 REMARK 500 O HOH A 910 O HOH A 1057 2.04 REMARK 500 O HOH A 714 O HOH A 1031 2.04 REMARK 500 O HOH A 535 O HOH A 694 2.05 REMARK 500 O HOH A 853 O HOH A 1072 2.12 REMARK 500 NZ LYS A 78 O HOH A 752 2.13 REMARK 500 O HOH A 699 O HOH A 914 2.16 REMARK 500 O HOH A 506 O HOH A 596 2.17 REMARK 500 O HOH A 919 O HOH A 1086 2.19 REMARK 500 O HOH A 724 O HOH A 926 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 194 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ASP A 230 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 366 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 9 -169.67 71.00 REMARK 500 ASP A 25 10.05 -67.35 REMARK 500 SER A 41 -144.80 -145.66 REMARK 500 PHE A 218 85.95 -155.69 REMARK 500 TYR A 221 -65.45 -95.51 REMARK 500 HIS A 233 171.23 70.61 REMARK 500 ASP A 262 -91.14 -119.77 REMARK 500 ASP A 281 6.49 -151.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 39 O REMARK 620 2 SER A 41 OG 99.6 REMARK 620 3 GLN A 43 O 106.6 67.7 REMARK 620 4 HOH A 713 O 144.3 89.3 108.8 REMARK 620 5 HOH A 716 O 62.7 140.7 148.4 88.7 REMARK 620 6 HOH A 971 O 57.7 80.5 142.0 90.4 60.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 105 OH REMARK 620 2 LYS A 190 O 85.3 REMARK 620 3 ILE A 193 O 103.8 90.4 REMARK 620 4 HOH A 644 O 161.0 90.9 94.9 REMARK 620 5 HOH A 798 O 91.8 176.6 92.1 91.2 REMARK 620 6 HOH A 805 O 85.1 89.8 171.1 76.2 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 135 O REMARK 620 2 SER A 176 O 103.7 REMARK 620 3 SER A 176 OG 172.9 82.5 REMARK 620 4 HOH A 578 O 80.7 82.2 96.8 REMARK 620 5 HOH A 630 O 90.0 164.1 83.5 92.2 REMARK 620 6 HOH A 748 O 100.5 93.3 82.5 175.5 92.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 406 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 241 O REMARK 620 2 SER A 259 OG 88.8 REMARK 620 3 THR A 260 O 172.9 95.3 REMARK 620 4 HOH A 576 O 170.7 95.4 2.5 REMARK 620 5 HOH A 706 O 166.3 97.7 6.7 4.4 REMARK 620 6 HOH A1045 O 169.3 91.5 6.2 4.6 6.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 407 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 288 O REMARK 620 2 LEU A 291 O 84.4 REMARK 620 3 HOH A 610 O 154.7 117.2 REMARK 620 4 HOH A 643 O 71.7 138.6 96.1 REMARK 620 5 HOH A 693 O 103.3 110.2 58.5 108.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FON A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T3Q A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 415 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XCZ RELATED DB: PDB REMARK 900 RELATED ID: 4XD0 RELATED DB: PDB DBREF 4XD1 A 1 397 UNP F8RC03 F8RC03_9ENTR 1 397 SEQADV 4XD1 MET A -19 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 GLY A -18 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 SER A -17 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 SER A -16 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 HIS A -15 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 HIS A -14 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 HIS A -13 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 HIS A -12 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 HIS A -11 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 HIS A -10 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 SER A -9 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 SER A -8 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 GLU A -7 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 ASN A -6 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 LEU A -5 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 TYR A -4 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 PHE A -3 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 GLN A -2 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 GLY A -1 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 ALA A 0 UNP F8RC03 EXPRESSION TAG SEQADV 4XD1 ALA A 305 UNP F8RC03 TRP 305 ENGINEERED MUTATION SEQRES 1 A 417 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLU SEQRES 2 A 417 ASN LEU TYR PHE GLN GLY ALA MET LYS LEU ILE ILE ALA SEQRES 3 A 417 GLY LYS ASN ASN ILE ALA VAL ASP VAL THR LYS TRP ILE SEQRES 4 A 417 ILE LYS THR ILE SER ASP ILE GLU LEU TYR SER VAL CYS SEQRES 5 A 417 ASN GLU ASN ASP HIS GLY ASN ASP SER PHE GLN LEU SER SEQRES 6 A 417 PHE LYS LYS PHE CYS ILE GLN PHE ASN ILE PRO ILE ILE SEQRES 7 A 417 SER LEU GLU ASP ALA TYR HIS LEU GLU ASP ALA ILE PHE SEQRES 8 A 417 LEU SER LEU GLU PHE ASP LYS ILE ILE HIS PRO SER LYS SEQRES 9 A 417 PHE THR HIS ASN ARG ILE PHE ASN ILE HIS PHE SER TYR SEQRES 10 A 417 LEU PRO ALA TYR LYS GLY MET TYR THR SER ALA TRP PRO SEQRES 11 A 417 ILE LEU ASN ASN GLU GLN GLU SER GLY VAL THR LEU HIS SEQRES 12 A 417 LYS ILE ASP HIS GLY ILE ASP THR GLY ALA ILE ILE ASP SEQRES 13 A 417 GLN GLN LYS PHE PRO LEU ASP ILE GLU GLU THR ALA LYS SEQRES 14 A 417 THR LEU TYR LEU LYS TYR ILE LYS ILE GLY THR GLU ILE SEQRES 15 A 417 VAL ILE LYS ASN LEU PRO ALA LEU ILE SER GLY ASN TYR SEQRES 16 A 417 SER ILE VAL GLU GLN SER ALA ILE LYS SER SER TYR TYR SEQRES 17 A 417 SER LYS LYS SER ILE ASP TYR LYS ASN LEU MET ILE ASP SEQRES 18 A 417 LEU ASN LYS THR ALA HIS GLU ILE LEU GLN GLN ILE ARG SEQRES 19 A 417 ALA PHE THR PHE ARG ASP TYR GLN LEU PRO ARG ILE ASP SEQRES 20 A 417 ASP ILE ASP ILE PHE HIS GLY GLU ILE LEU SER SER LYS SEQRES 21 A 417 SER LEU SER LYS PRO GLY THR ILE LEU GLU LYS ASN ASN SEQRES 22 A 417 TYR HIS LEU ILE LEU SER THR ILE ASP TYR ASP ILE LYS SEQRES 23 A 417 LEU TYR SER ASP ASN PHE ASP GLU ILE LEU THR ALA CYS SEQRES 24 A 417 GLU ASP LYS SER PRO GLU PHE ILE SER LYS LEU LEU LYS SEQRES 25 A 417 THR GLU ASN ILE LEU PHE GLU LYS ASN HIS LEU GLY ALA SEQRES 26 A 417 SER PRO ILE ILE ILE ALA ALA TYR HIS GLY ASN MET ASP SEQRES 27 A 417 VAL ILE GLU TRP LEU VAL SER LYS GLY VAL ASN ILE ASN SEQRES 28 A 417 ASP ARG ASN TYR LYS GLY THR THR VAL ALA MET TYR PHE SEQRES 29 A 417 LYS ASP TYR MET LEU ARG SER GLY ASN TYR THR GLY LEU SEQRES 30 A 417 GLU ASN LEU ILE ASN LEU GLY LEU ASP LEU PHE LEU LYS SEQRES 31 A 417 ASP ASN GLU GLY LEU SER VAL PHE ASP TYR MET ARG LYS SEQRES 32 A 417 ASN LYS ASN ILE GLU LEU PHE ASN PHE MET SER THR PHE SEQRES 33 A 417 ASN HET FON A 401 34 HET T3Q A 402 35 HET NA A 403 1 HET NA A 404 1 HET NA A 405 1 HET K A 406 1 HET NA A 407 1 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET CL A 413 1 HET CL A 414 1 HET CL A 415 1 HETNAM FON N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8- HETNAM 2 FON HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}- HETNAM 3 FON L-GLUTAMIC ACID HETNAM T3Q [(3R,4S,5S,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2- HETNAM 2 T3Q YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4- HETNAM 3 T3Q DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL] HETNAM 4 T3Q HYDROGEN PHOSPHATE HETNAM NA SODIUM ION HETNAM K POTASSIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN FON [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE; 6R-FOLINIC ACID HETSYN T3Q THYMIDINE-5'-DIPHOSPHATE-ALPHA-D-3,6-DIDEOXY-3- HETSYN 2 T3Q AMINOGLUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 FON C20 H23 N7 O7 FORMUL 3 T3Q C16 H27 N3 O14 P2 FORMUL 4 NA 4(NA 1+) FORMUL 7 K K 1+ FORMUL 9 EDO 5(C2 H6 O2) FORMUL 14 CL 3(CL 1-) FORMUL 17 HOH *605(H2 O) HELIX 1 AA1 LYS A 8 ILE A 23 1 16 HELIX 2 AA2 SER A 45 PHE A 53 1 9 HELIX 3 AA3 SER A 59 LEU A 66 1 8 HELIX 4 AA4 HIS A 81 PHE A 85 5 5 HELIX 5 AA5 ALA A 108 ASN A 113 1 6 HELIX 6 AA6 THR A 147 GLY A 173 1 27 HELIX 7 AA7 SER A 189 ILE A 193 5 5 HELIX 8 AA8 THR A 205 PHE A 216 1 12 HELIX 9 AA9 ASN A 271 GLU A 280 1 10 HELIX 10 AB1 SER A 283 LEU A 291 1 9 HELIX 11 AB2 THR A 293 GLU A 299 5 7 HELIX 12 AB3 SER A 306 HIS A 314 1 9 HELIX 13 AB4 ASN A 316 LYS A 326 1 11 HELIX 14 AB5 THR A 339 GLY A 352 1 14 HELIX 15 AB6 GLY A 356 LEU A 363 1 8 HELIX 16 AB7 SER A 376 ASN A 384 1 9 HELIX 17 AB8 ASN A 386 THR A 395 1 10 SHEET 1 AA1 6 GLU A 27 CYS A 32 0 SHEET 2 AA1 6 LYS A 2 GLY A 7 1 N ILE A 5 O TYR A 29 SHEET 3 AA1 6 ALA A 69 LEU A 74 1 O ILE A 70 N ILE A 4 SHEET 4 AA1 6 ILE A 90 HIS A 94 1 O PHE A 91 N SER A 73 SHEET 5 AA1 6 GLU A 117 LYS A 124 -1 O THR A 121 N HIS A 94 SHEET 6 AA1 6 ILE A 134 PRO A 141 -1 O ASP A 136 N LEU A 122 SHEET 1 AA2 2 LYS A 102 GLY A 103 0 SHEET 2 AA2 2 TYR A 187 TYR A 188 1 O TYR A 188 N LYS A 102 SHEET 1 AA3 5 ARG A 225 ILE A 226 0 SHEET 2 AA3 5 ILE A 229 ILE A 236 -1 O ILE A 229 N ILE A 226 SHEET 3 AA3 5 ILE A 265 SER A 269 -1 O LYS A 266 N GLU A 235 SHEET 4 AA3 5 HIS A 255 LEU A 258 -1 N LEU A 256 O LEU A 267 SHEET 5 AA3 5 ILE A 248 LYS A 251 -1 N LEU A 249 O ILE A 257 LINK O ASN A 39 NA NA A 403 1555 1555 3.08 LINK OG SER A 41 NA NA A 403 1555 1555 3.13 LINK O GLN A 43 NA NA A 403 1555 1555 2.70 LINK OH TYR A 105 NA NA A 405 1555 1555 2.49 LINK O ILE A 135 NA NA A 404 1555 1555 2.27 LINK O SER A 176 NA NA A 404 1555 1555 2.45 LINK OG SER A 176 NA NA A 404 1555 1555 2.40 LINK O LYS A 190 NA NA A 405 1555 1555 2.29 LINK O ILE A 193 NA NA A 405 1555 1555 2.32 LINK O SER A 241 K K A 406 1555 8665 2.32 LINK OG SER A 259 K K A 406 1555 8665 2.58 LINK O THR A 260 K K A 406 1555 8665 2.31 LINK O SER A 288 NA NA A 407 1555 1555 2.97 LINK O LEU A 291 NA NA A 407 1555 1555 2.51 LINK NA NA A 403 O HOH A 713 1555 1555 2.81 LINK NA NA A 403 O HOH A 716 1555 1555 3.01 LINK NA NA A 403 O HOH A 971 1555 1555 2.95 LINK NA NA A 404 O HOH A 578 1555 1555 2.50 LINK NA NA A 404 O HOH A 630 1555 1555 2.34 LINK NA NA A 404 O HOH A 748 1555 1555 2.47 LINK NA NA A 405 O HOH A 644 1555 1555 2.44 LINK NA NA A 405 O HOH A 798 1555 1555 2.39 LINK NA NA A 405 O HOH A 805 1555 1555 2.49 LINK K K A 406 O HOH A 576 1555 8665 2.39 LINK K K A 406 O HOH A 706 1555 8665 2.38 LINK K K A 406 O HOH A1045 1555 8665 2.43 LINK NA NA A 407 O HOH A 610 1555 5555 2.59 LINK NA NA A 407 O HOH A 643 1555 1555 2.73 LINK NA NA A 407 O HOH A 693 1555 1555 2.97 CISPEP 1 LEU A 98 PRO A 99 0 13.51 SITE 1 AC1 18 PHE A 76 ASP A 77 LYS A 78 ILE A 79 SITE 2 AC1 18 ILE A 80 ASP A 126 HIS A 127 GLY A 128 SITE 3 AC1 18 ILE A 129 ASP A 130 TYR A 187 SER A 189 SITE 4 AC1 18 LYS A 190 T3Q A 402 HOH A 501 HOH A 721 SITE 5 AC1 18 HOH A 723 HOH A 926 SITE 1 AC2 26 LYS A 8 GLU A 75 PHE A 76 GLY A 103 SITE 2 AC2 26 MET A 104 TYR A 105 THR A 106 SER A 107 SITE 3 AC2 26 TYR A 152 TYR A 195 PHE A 218 TYR A 221 SITE 4 AC2 26 GLN A 222 FON A 401 HOH A 606 HOH A 717 SITE 5 AC2 26 HOH A 718 HOH A 719 HOH A 720 HOH A 721 SITE 6 AC2 26 HOH A 722 HOH A 806 HOH A 809 HOH A 905 SITE 7 AC2 26 HOH A 964 HOH A 965 SITE 1 AC3 6 ASN A 39 SER A 41 GLN A 43 HOH A 713 SITE 2 AC3 6 HOH A 716 HOH A 971 SITE 1 AC4 5 ILE A 135 SER A 176 HOH A 578 HOH A 630 SITE 2 AC4 5 HOH A 748 SITE 1 AC5 6 TYR A 105 LYS A 190 ILE A 193 HOH A 644 SITE 2 AC5 6 HOH A 798 HOH A 805 SITE 1 AC6 6 SER A 241 SER A 259 THR A 260 HOH A 576 SITE 2 AC6 6 HOH A 706 HOH A1045 SITE 1 AC7 5 SER A 288 LEU A 291 HOH A 610 HOH A 643 SITE 2 AC7 5 HOH A 693 SITE 1 AC8 6 LYS A 149 PHE A 298 GLU A 299 HOH A 732 SITE 2 AC8 6 HOH A 735 HOH A 975 SITE 1 AC9 7 PRO A 99 GLU A 179 SER A 181 LYS A 289 SITE 2 AC9 7 HOH A 532 HOH A 681 HOH A 794 SITE 1 AD1 8 TYR A 254 ASN A 271 LEU A 290 LYS A 292 SITE 2 AD1 8 HOH A 567 HOH A 705 HOH A 838 HOH A1012 SITE 1 AD2 3 ILE A 26 LEU A 28 PRO A 56 SITE 1 AD3 8 TRP A 109 TYR A 188 SER A 192 LYS A 204 SITE 2 AD3 8 HOH A 505 HOH A 521 HOH A 558 HOH A 823 SITE 1 AD4 2 ILE A 387 GLU A 388 SITE 1 AD5 5 LYS A 345 MET A 381 ASN A 384 ASN A 386 SITE 2 AD5 5 HOH A 903 SITE 1 AD6 3 LYS A 8 ASN A 33 HOH A 963 CRYST1 78.279 78.279 151.105 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006618 0.00000