HEADER TRANSFERASE 09-DEC-18 6NBP TITLE CRYSTAL STRUCTURE OF A SUGAR N-FORMYLTRANSFERASE FROM THE PLANT TITLE 2 PATHOGEN PANTOEA ANANATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-FORMYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PANTOEA ANANATIS; SOURCE 3 ORGANISM_TAXID: 553; SOURCE 4 STRAIN: NFR11; SOURCE 5 GENE: SAMN03097714_1080; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3) KEYWDS SUGAR BIOSYNTHESIS, O-ANTIGEN, PANTOEA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.L.HOFMEISTER,J.B.THODEN,H.M.HOLDEN REVDAT 6 11-OCT-23 6NBP 1 LINK REVDAT 5 01-JAN-20 6NBP 1 REMARK REVDAT 4 17-APR-19 6NBP 1 REMARK REVDAT 3 03-APR-19 6NBP 1 JRNL REVDAT 2 06-FEB-19 6NBP 1 JRNL REVDAT 1 19-DEC-18 6NBP 0 JRNL AUTH D.L.HOFMEISTER,J.B.THODEN,H.M.HOLDEN JRNL TITL INVESTIGATION OF A SUGAR N-FORMYLTRANSFERASE FROM THE PLANT JRNL TITL 2 PATHOGEN PANTOEA ANANATIS. JRNL REF PROTEIN SCI. V. 28 707 2019 JRNL REFN ESSN 1469-896X JRNL PMID 30666752 JRNL DOI 10.1002/PRO.3577 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 30727 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1537 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2096 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE SET COUNT : 107 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1965 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : -1.56000 REMARK 3 B12 (A**2) : 0.24000 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): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.943 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2095 ; 0.011 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 1846 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2848 ; 1.554 ; 1.770 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4330 ; 0.504 ; 1.720 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ; 6.786 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;35.091 ;20.345 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 311 ;16.251 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;21.798 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 288 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2335 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 395 ; 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): 990 ; 2.248 ; 2.517 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 991 ; 2.247 ; 2.518 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1236 ; 3.390 ; 3.753 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1237 ; 3.388 ; 3.754 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1105 ; 2.875 ; 2.834 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1102 ; 2.820 ; 2.819 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1602 ; 4.395 ; 4.113 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2370 ; 6.407 ;31.360 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2296 ; 6.312 ;30.686 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 : NULL 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 6NBP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1000238515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : 32264 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : 0.43300 REMARK 200 FOR SHELL : 2.100 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: 4YFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13-16%PEG-3350, 2 MM FOLINIC ACID, 5 REMARK 280 MM DTDP-QUI4N, 200 MM NACL, 100 MM HEPES, PH 8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.19700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.39400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.39400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.19700 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: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -29.19700 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 539 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 593 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 GLY A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLN A 3 REMARK 465 VAL A 4 REMARK 465 SER A 5 REMARK 465 LYS A 6 REMARK 465 VAL A 7 REMARK 465 ALA A 8 REMARK 465 THR A 9 REMARK 465 ASP A 10 REMARK 465 ALA A 11 REMARK 465 ARG A 12 REMARK 465 GLU A 144 REMARK 465 VAL A 145 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 13 CG CD1 CD2 REMARK 470 PHE A 55 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 245 CG CD OE1 OE2 REMARK 470 LYS A 246 CG CD CE NZ REMARK 470 ARG A 248 CG CD NE CZ NH1 NH2 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 O HOH A 591 O HOH A 598 2.11 REMARK 500 O3 FON A 302 O HOH A 401 2.12 REMARK 500 OD1 ASP A 223 O2 PO4 A 304 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 528 O HOH A 592 4555 2.10 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 THR A 57 -115.45 -92.62 REMARK 500 LEU A 91 78.87 -102.81 REMARK 500 ASN A 239 -74.54 -103.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 44 0.14 SIDE CHAIN REMARK 500 ARG A 249 0.24 SIDE CHAIN REMARK 500 ARG A 253 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 651 DISTANCE = 7.07 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 FON A 302 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 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 151 O REMARK 620 2 THR A 192 O 108.0 REMARK 620 3 THR A 192 OG1 144.1 36.3 REMARK 620 4 HOH A 539 O 174.3 70.5 34.2 REMARK 620 5 HOH A 539 O 174.3 70.5 34.2 0.0 REMARK 620 6 HOH A 596 O 118.3 123.4 93.9 66.2 66.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0FX A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FON A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 304 DBREF 6NBP A -2 260 PDB 6NBP 6NBP -2 260 SEQRES 1 A 263 GLY GLY HIS MET THR GLN VAL SER LYS VAL ALA THR ASP SEQRES 2 A 263 ALA ARG LEU THR ALA GLN ALA GLN ARG LEU LEU VAL VAL SEQRES 3 A 263 SER ASP ASN GLN GLU LEU SER LEU TYR LEU LYS GLU GLU SEQRES 4 A 263 LEU GLU LYS GLN SER PHE GLU ARG PRO PHE ASN ALA ASP SEQRES 5 A 263 PHE CYS TYR THR SER PHE ASN THR ASN PRO GLN GLN MET SEQRES 6 A 263 MET ALA MET GLY ALA THR LYS ILE ASN ILE LYS ASP GLU SEQRES 7 A 263 PHE THR VAL GLU ARG ILE ILE ASN GLU TYR ASP LEU VAL SEQRES 8 A 263 PHE SER LEU HIS CYS LYS GLN ILE PHE PRO ALA LYS LEU SEQRES 9 A 263 THR ASP ASN VAL CYS CYS ILE ASN PHE HIS PRO GLY LEU SEQRES 10 A 263 ASN PRO TYR ASN ARG GLY TRP TYR PRO GLN ALA PHE SER SEQRES 11 A 263 ILE ILE ASN GLY LEU PRO THR GLY ALA THR ILE HIS LEU SEQRES 12 A 263 MET ASP ALA GLU VAL ASP HIS GLY ASP ILE ILE ASP GLN SEQRES 13 A 263 GLN GLU VAL GLU VAL LYS MET SER ASP THR SER LEU THR SEQRES 14 A 263 VAL TYR ARG LYS VAL ILE ALA ILE GLU LYS HIS LEU ILE SEQRES 15 A 263 SER ARG ASN ILE PHE THR ILE ILE THR ARG SER TYR THR SEQRES 16 A 263 THR LYS LYS PRO GLN ALA GLU GLY ASN TYR ASN GLY ILE SEQRES 17 A 263 LYS ASP PHE ASN ALA LEU CYS GLU LEU ASP LEU ASN SER SEQRES 18 A 263 ILE GLY THR LEU ASP GLU HIS LEU LYS ILE LEU ARG ALA SEQRES 19 A 263 THR THR HIS GLY ASP PHE LYS ASN ALA PHE PHE CYS ASP SEQRES 20 A 263 GLU LYS GLY ARG ARG PHE PHE VAL ARG ILE VAL ILE ASP SEQRES 21 A 263 GLU ALA PHE HET 0FX A 301 35 HET FON A 302 15 HET NA A 303 1 HET PO4 A 304 5 HETNAM 0FX DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE 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 NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETSYN FON [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE; 6R-FOLINIC ACID FORMUL 2 0FX C16 H27 N3 O14 P2 FORMUL 3 FON C20 H23 N7 O7 FORMUL 4 NA NA 1+ FORMUL 5 PO4 O4 P 3- FORMUL 6 HOH *251(H2 O) HELIX 1 AA1 ASN A 26 LYS A 39 1 14 HELIX 2 AA2 ASN A 58 MET A 65 1 8 HELIX 3 AA3 ASP A 74 TYR A 85 1 12 HELIX 4 AA4 PRO A 98 ASP A 103 1 6 HELIX 5 AA5 TYR A 122 GLY A 131 1 10 HELIX 6 AA6 THR A 163 THR A 188 1 26 HELIX 7 AA7 GLY A 204 GLU A 213 1 10 HELIX 8 AA8 THR A 221 THR A 233 1 13 SHEET 1 AA1 7 THR A 68 LYS A 69 0 SHEET 2 AA1 7 ASN A 47 TYR A 52 1 N TYR A 52 O THR A 68 SHEET 3 AA1 7 ARG A 19 SER A 24 1 N VAL A 22 O ASP A 49 SHEET 4 AA1 7 LEU A 87 LEU A 91 1 O PHE A 89 N VAL A 23 SHEET 5 AA1 7 CYS A 107 HIS A 111 1 O ILE A 108 N SER A 90 SHEET 6 AA1 7 THR A 134 LEU A 140 -1 O HIS A 139 N ASN A 109 SHEET 7 AA1 7 ILE A 150 VAL A 156 -1 O ASP A 152 N ILE A 138 SHEET 1 AA2 2 ARG A 119 GLY A 120 0 SHEET 2 AA2 2 TYR A 202 ASN A 203 1 O ASN A 203 N ARG A 119 SHEET 1 AA3 2 ALA A 240 CYS A 243 0 SHEET 2 AA3 2 ARG A 249 VAL A 252 -1 O PHE A 250 N PHE A 242 LINK O ILE A 151 NA NA A 303 1555 1555 2.68 LINK O THR A 192 NA NA A 303 1555 1555 2.95 LINK OG1 THR A 192 NA NA A 303 1555 5555 2.93 LINK NA NA A 303 O HOH A 539 1555 1555 3.18 LINK NA NA A 303 O HOH A 539 1555 5555 3.18 LINK NA NA A 303 O HOH A 596 1555 5555 2.44 CISPEP 1 ASN A 115 PRO A 116 0 8.59 SITE 1 AC1 26 GLN A 60 MET A 63 HIS A 92 CYS A 93 SITE 2 AC1 26 LYS A 94 HIS A 111 GLY A 120 TRP A 121 SITE 3 AC1 26 TYR A 122 GLN A 124 TYR A 168 HIS A 234 SITE 4 AC1 26 PHE A 237 ASN A 239 FON A 302 HOH A 401 SITE 5 AC1 26 HOH A 418 HOH A 433 HOH A 444 HOH A 445 SITE 6 AC1 26 HOH A 454 HOH A 477 HOH A 481 HOH A 547 SITE 7 AC1 26 HOH A 557 HOH A 588 SITE 1 AC2 9 SER A 90 CYS A 93 GLN A 95 PHE A 97 SITE 2 AC2 9 ASN A 109 MET A 141 0FX A 301 HOH A 401 SITE 3 AC2 9 HOH A 556 SITE 1 AC3 3 ILE A 151 THR A 192 HOH A 596 SITE 1 AC4 6 MET A 160 ASP A 223 LEU A 226 LYS A 227 SITE 2 AC4 6 ARG A 230 PHE A 242 CRYST1 75.928 75.928 87.591 90.00 90.00 120.00 P 31 2 1 6 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 0.013170 0.007604 0.000000 0.00000 SCALE2 0.000000 0.015208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011417 0.00000