HEADER TRANSFERASE 18-DEC-14 4XD0 TITLE X-RAY STRUCTURE OF THE N-FORMYLTRANSFERASE QDTF FROM PROVIDENCIA TITLE 2 ALCALIFACIENS 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 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 4XD0 1 SOURCE JRNL REMARK LINK REVDAT 3 11-FEB-15 4XD0 1 JRNL REVDAT 2 04-FEB-15 4XD0 1 JRNL REVDAT 1 21-JAN-15 4XD0 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 40092 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2131 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2710 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.4010 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3236 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 109 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31000 REMARK 3 B22 (A**2) : 1.31000 REMARK 3 B33 (A**2) : -2.61000 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): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.815 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3430 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3237 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4657 ; 1.777 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7474 ; 0.807 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 6.529 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;37.281 ;25.409 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 610 ;15.029 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;16.048 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 520 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3790 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 783 ; 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 4XD0 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_1000205460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-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 : 42223 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 95.4 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 48.73 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 SODIUM CHLORIDE, 200 MM POTASSIUM CHLORIDE, 5 MM TDP, 5 MM N5- REMARK 280 THF, PH 8, VAPOR DIFFUSION, 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 75.71200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.06700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.06700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.85600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.06700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.06700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.56800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.06700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.06700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.85600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.06700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.06700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.56800 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 75.71200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL 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 BIOMT1 2 0.000000 -1.000000 0.000000 78.13400 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 78.13400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.71200 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 558 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 600 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 OD2 ASP A 62 O HOH A 826 1.97 REMARK 500 O HOH A 510 O HOH A 518 1.99 REMARK 500 O HOH A 664 O HOH A 729 2.04 REMARK 500 OH TYR A 335 O HOH A 756 2.05 REMARK 500 O HOH A 607 O HOH A 729 2.07 REMARK 500 O HOH A 584 O HOH A 652 2.07 REMARK 500 O HOH A 525 O HOH A 597 2.15 REMARK 500 O HOH A 629 O HOH A 811 2.16 REMARK 500 OD1 ASP A 194 O HOH A 501 2.18 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 201 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 201 CB - CG - OD2 ANGL. DEV. = -5.5 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 -170.36 70.67 REMARK 500 ASP A 25 -16.30 83.55 REMARK 500 SER A 41 -143.18 -137.54 REMARK 500 SER A 118 -159.77 -143.02 REMARK 500 ASP A 126 -169.64 -118.42 REMARK 500 PHE A 218 87.19 -151.33 REMARK 500 HIS A 233 175.86 69.33 REMARK 500 ASP A 262 -97.16 -117.17 REMARK 500 ASP A 281 12.86 -151.65 REMARK 500 ASN A 386 74.28 -107.38 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 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 105 OH REMARK 620 2 LYS A 190 O 77.0 REMARK 620 3 ILE A 193 O 100.5 90.2 REMARK 620 4 HOH A 579 O 163.8 93.4 92.4 REMARK 620 5 HOH A 753 O 96.1 173.1 91.2 93.3 REMARK 620 6 HOH A 754 O 84.0 90.2 175.5 83.1 88.8 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 ILE A 135 O REMARK 620 2 SER A 176 O 110.2 REMARK 620 3 SER A 176 OG 162.2 84.0 REMARK 620 4 HOH A 531 O 76.3 84.4 95.3 REMARK 620 5 HOH A 540 O 87.3 161.3 77.6 93.8 REMARK 620 6 HOH A 673 O 100.0 100.4 87.3 174.8 82.4 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 LYS A 196 O REMARK 620 2 ASN A 384 O 83.9 REMARK 620 3 LYS A 385 O 83.7 2.0 REMARK 620 4 ASN A 386 OD1 85.3 4.4 2.8 REMARK 620 5 HOH A 569 O 86.8 4.4 3.4 1.8 REMARK 620 6 HOH A 587 O 89.4 5.7 5.7 4.7 2.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 241 O REMARK 620 2 SER A 243 O 84.0 REMARK 620 3 SER A 259 OG 99.4 58.8 REMARK 620 4 THR A 260 O 157.8 118.2 93.4 REMARK 620 5 HOH A 589 O 88.7 78.2 134.8 95.1 REMARK 620 6 HOH A 621 O 91.7 138.3 81.3 72.3 143.3 REMARK 620 7 HOH A 809 O 70.6 139.0 154.4 90.2 69.8 75.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T3F A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FON A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T3F A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K 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 NA 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 CL A 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XCZ RELATED DB: PDB REMARK 900 RELATED ID: 4XD1 RELATED DB: PDB DBREF 4XD0 A 1 397 UNP F8RC03 F8RC03_9ENTR 1 397 SEQADV 4XD0 MET A -19 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 GLY A -18 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 SER A -17 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 SER A -16 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 HIS A -15 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 HIS A -14 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 HIS A -13 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 HIS A -12 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 HIS A -11 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 HIS A -10 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 SER A -9 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 SER A -8 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 GLU A -7 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 ASN A -6 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 LEU A -5 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 TYR A -4 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 PHE A -3 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 GLN A -2 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 GLY A -1 UNP F8RC03 EXPRESSION TAG SEQADV 4XD0 ALA A 0 UNP F8RC03 EXPRESSION TAG 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 TRP 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 T3F A 401 35 HET FON A 402 34 HET T3F A 403 35 HET K A 404 1 HET NA A 405 1 HET NA A 406 1 HET NA A 407 1 HET CL A 408 1 HETNAM T3F (3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2- HETNAM 2 T3F YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4- HETNAM 3 T3F DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL] HETNAM 4 T3F HYDROGEN PHOSPHATE 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 K POTASSIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN T3F THYMIDINE-5'-DIPHOSPHATE-ALPHA-D-3,6-DIDEOXY-3- HETSYN 2 T3F AMINOGALACTOSE HETSYN FON [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE; 6R-FOLINIC ACID FORMUL 2 T3F 2(C16 H27 N3 O14 P2) FORMUL 3 FON C20 H23 N7 O7 FORMUL 5 K K 1+ FORMUL 6 NA 3(NA 1+) FORMUL 9 CL CL 1- FORMUL 10 HOH *337(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 HIS A 65 1 7 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 ASP A 194 LEU A 198 5 5 HELIX 9 AA9 THR A 205 PHE A 216 1 12 HELIX 10 AB1 ASN A 271 LYS A 282 1 12 HELIX 11 AB2 SER A 283 LEU A 291 1 9 HELIX 12 AB3 THR A 293 GLU A 299 5 7 HELIX 13 AB4 SER A 306 HIS A 314 1 9 HELIX 14 AB5 ASN A 316 LYS A 326 1 11 HELIX 15 AB6 THR A 339 GLY A 352 1 14 HELIX 16 AB7 GLY A 356 GLY A 364 1 9 HELIX 17 AB8 SER A 376 ASN A 384 1 9 HELIX 18 AB9 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 HIS A 123 N ASN A 92 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 OH TYR A 105 NA NA A 406 1555 1555 2.64 LINK O ILE A 135 NA NA A 407 1555 1555 2.42 LINK O SER A 176 NA NA A 407 1555 1555 2.40 LINK OG SER A 176 NA NA A 407 1555 1555 2.39 LINK O LYS A 190 NA NA A 406 1555 1555 2.41 LINK O ILE A 193 NA NA A 406 1555 1555 2.27 LINK O LYS A 196 NA NA A 405 1555 7465 2.71 LINK O SER A 241 K K A 404 1555 1555 2.79 LINK O SER A 243 K K A 404 1555 1555 3.12 LINK OG SER A 259 K K A 404 1555 1555 2.73 LINK O THR A 260 K K A 404 1555 1555 2.48 LINK O ASN A 384 NA NA A 405 1555 1555 2.79 LINK O LYS A 385 NA NA A 405 1555 1555 2.93 LINK OD1 ASN A 386 NA NA A 405 1555 1555 3.11 LINK K K A 404 O HOH A 589 1555 1555 2.96 LINK K K A 404 O HOH A 621 1555 1555 2.95 LINK K K A 404 O HOH A 809 1555 1555 2.24 LINK NA NA A 405 O HOH A 569 1555 1555 2.77 LINK NA NA A 405 O HOH A 587 1555 7465 2.68 LINK NA NA A 406 O HOH A 579 1555 1555 2.57 LINK NA NA A 406 O HOH A 753 1555 1555 2.35 LINK NA NA A 406 O HOH A 754 1555 1555 2.34 LINK NA NA A 407 O HOH A 531 1555 1555 2.60 LINK NA NA A 407 O HOH A 540 1555 1555 2.06 LINK NA NA A 407 O HOH A 673 1555 1555 2.48 CISPEP 1 LEU A 98 PRO A 99 0 15.89 SITE 1 AC1 15 HIS A 302 TRP A 305 ILE A 310 TYR A 313 SITE 2 AC1 15 HIS A 314 ASN A 334 LYS A 336 THR A 338 SITE 3 AC1 15 TYR A 343 ASP A 346 TYR A 380 HOH A 604 SITE 4 AC1 15 HOH A 630 HOH A 749 HOH A 750 SITE 1 AC2 16 PHE A 76 ASP A 77 LYS A 78 ILE A 79 SITE 2 AC2 16 ILE A 80 ASP A 126 GLY A 128 ILE A 129 SITE 3 AC2 16 ASP A 130 TYR A 187 LYS A 190 T3F A 403 SITE 4 AC2 16 HOH A 609 HOH A 612 HOH A 670 HOH A 730 SITE 1 AC3 23 LYS A 8 GLU A 75 PHE A 76 GLY A 103 SITE 2 AC3 23 TYR A 105 THR A 106 SER A 107 TYR A 152 SITE 3 AC3 23 TYR A 195 PHE A 218 TYR A 221 GLN A 222 SITE 4 AC3 23 FON A 402 HOH A 605 HOH A 614 HOH A 616 SITE 5 AC3 23 HOH A 622 HOH A 639 HOH A 641 HOH A 663 SITE 6 AC3 23 HOH A 709 HOH A 728 HOH A 816 SITE 1 AC4 7 SER A 241 SER A 243 SER A 259 THR A 260 SITE 2 AC4 7 HOH A 589 HOH A 621 HOH A 809 SITE 1 AC5 6 LYS A 196 ASN A 384 LYS A 385 ASN A 386 SITE 2 AC5 6 HOH A 569 HOH A 587 SITE 1 AC6 6 TYR A 105 LYS A 190 ILE A 193 HOH A 579 SITE 2 AC6 6 HOH A 753 HOH A 754 SITE 1 AC7 5 ILE A 135 SER A 176 HOH A 531 HOH A 540 SITE 2 AC7 5 HOH A 673 SITE 1 AC8 4 LYS A 345 MET A 381 ASN A 384 ASN A 386 CRYST1 78.134 78.134 151.424 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 0.012799 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006604 0.00000