HEADER LIGASE 18-OCT-14 4RM2 TITLE CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE WITH 2-FLUORO TITLE 2 BENZOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: BENZOATE-COENZYME A LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS; SOURCE 3 ORGANISM_TAXID: 1076; SOURCE 4 GENE: BADA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS SUBSTRATE SPECIFICITY, KINETICS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.STROM,M.NOSRATI,C.THORNBURG,K.D.WALKER,J.H.GEIGER REVDAT 4 20-SEP-23 4RM2 1 REMARK SEQADV REVDAT 3 11-NOV-15 4RM2 1 JRNL REVDAT 2 07-OCT-15 4RM2 1 JRNL REVDAT 1 30-SEP-15 4RM2 0 JRNL AUTH C.K.THORNBURG,S.WORTAS-STROM,M.NOSRATI,J.H.GEIGER,K.D.WALKER JRNL TITL KINETICALLY AND CRYSTALLOGRAPHICALLY GUIDED MUTATIONS OF A JRNL TITL 2 BENZOATE COA LIGASE (BADA) ELUCIDATE MECHANISM AND EXPAND JRNL TITL 3 SUBSTRATE PERMISSIVITY. JRNL REF BIOCHEMISTRY V. 54 6230 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26378464 JRNL DOI 10.1021/ACS.BIOCHEM.5B00899 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 92653 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4931 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5612 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 295 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7851 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 738 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.668 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8156 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7662 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11141 ; 1.961 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17614 ; 0.943 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1053 ; 6.596 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 338 ;34.708 ;22.899 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1213 ;13.037 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 58 ;18.490 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1233 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9345 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1877 ; 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): 4158 ; 1.877 ; 1.766 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4157 ; 1.876 ; 1.765 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5199 ; 2.673 ; 2.639 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 5061 ; 2.370 ; 2.522 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3998 ; 2.611 ; 2.012 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3929 ; 2.569 ; 1.966 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5822 ; 3.875 ; 2.840 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9391 ; 5.232 ;14.496 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9058 ; 5.063 ;14.132 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 4RM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000087513. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92681 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 12.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.47500 REMARK 200 R SYM FOR SHELL (I) : 0.43700 REMARK 200 FOR SHELL : 1.550 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOL REP REMARK 200 STARTING MODEL: 2V7B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % PEG 3350, 0.1 M TRIS PH7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 47.87450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 VAL A 522 REMARK 465 LEU A 523 REMARK 465 GLY A 524 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 GLU A 156 CG CD OE1 OE2 REMARK 470 LYS A 166 CG CD CE NZ REMARK 470 ARG A 250 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 309 CG CD OE1 OE2 REMARK 470 ARG A 394 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 479 CG CD OE1 OE2 REMARK 470 LYS A 483 CG CD CE NZ REMARK 470 LYS A 487 CG CD CE NZ REMARK 470 LYS B 12 CG CD CE NZ REMARK 470 ARG B 390 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 394 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 398 CG CD OE1 NE2 REMARK 470 GLN B 475 CG CD OE1 NE2 REMARK 470 THR B 476 OG1 CG2 REMARK 470 SER B 478 OG REMARK 470 GLU B 479 CG CD OE1 OE2 REMARK 470 THR B 480 OG1 CG2 REMARK 470 LYS B 483 CG CD CE NZ REMARK 470 ILE B 486 CG1 CG2 CD1 REMARK 470 LYS B 487 CG CD CE NZ REMARK 470 ARG B 497 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 NH2 ARG A 489 OD2 ASP B 488 1.88 REMARK 500 O LYS A 487 O HOH A 1356 2.04 REMARK 500 O HOH B 1185 O HOH B 1469 2.12 REMARK 500 O HOH A 1215 O HOH A 1394 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER B 184 CB SER B 184 OG -0.078 REMARK 500 GLU B 309 CG GLU B 309 CD 0.110 REMARK 500 GLU B 309 CD GLU B 309 OE1 0.111 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 35 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 215 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 324 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 390 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 421 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 110 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 187 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 207 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP B 215 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 324 CB - CG - OD1 ANGL. DEV. = 5.4 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 GLU A 63 -13.05 78.80 REMARK 500 TYR A 205 -65.10 -108.71 REMARK 500 LEU A 234 -66.11 -146.71 REMARK 500 LEU A 332 -44.88 75.43 REMARK 500 ASP A 424 -18.13 79.35 REMARK 500 LEU A 477 116.48 -162.56 REMARK 500 GLU A 520 -114.08 -64.36 REMARK 500 ASP B 34 -165.12 -129.64 REMARK 500 GLU B 63 -12.46 77.92 REMARK 500 TYR B 205 -62.08 -106.21 REMARK 500 LEU B 234 -71.53 -141.82 REMARK 500 LEU B 332 -42.81 73.43 REMARK 500 ASP B 424 -3.06 74.17 REMARK 500 GLN B 475 -69.64 -95.14 REMARK 500 THR B 476 123.60 66.32 REMARK 500 LEU B 490 -143.76 -176.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR B 476 LEU B 477 -148.68 REMARK 500 ARG B 489 LEU B 490 136.80 REMARK 500 LEU B 490 ALA B 491 -144.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3U4 A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3U4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3U4 B 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EAT RELATED DB: PDB REMARK 900 RELATED ID: 4RLF RELATED DB: PDB REMARK 900 RELATED ID: 4RLQ RELATED DB: PDB REMARK 900 RELATED ID: 2V7B RELATED DB: PDB DBREF 4RM2 A 6 523 UNP Q93TK0 Q93TK0_RHOPL 5 522 DBREF 4RM2 B 6 523 UNP Q93TK0 Q93TK0_RHOPL 5 522 SEQADV 4RM2 ALA A 83 UNP Q93TK0 THR 82 CONFLICT SEQADV 4RM2 ASP A 341 UNP Q93TK0 GLY 340 CONFLICT SEQADV 4RM2 GLY A 524 UNP Q93TK0 EXPRESSION TAG SEQADV 4RM2 ALA B 83 UNP Q93TK0 THR 82 CONFLICT SEQADV 4RM2 ASP B 341 UNP Q93TK0 GLY 340 CONFLICT SEQADV 4RM2 GLY B 524 UNP Q93TK0 EXPRESSION TAG SEQRES 1 A 519 VAL THR PRO PRO PRO GLU LYS PHE ASN PHE ALA GLU HIS SEQRES 2 A 519 LEU LEU GLN THR ASN ARG VAL ARG PRO ASP LYS THR ALA SEQRES 3 A 519 PHE VAL ASP ASP ILE SER SER LEU SER PHE ALA GLN LEU SEQRES 4 A 519 GLU ALA GLN THR ARG GLN LEU ALA ALA ALA LEU ARG ALA SEQRES 5 A 519 ILE GLY VAL LYS ARG GLU GLU ARG VAL LEU LEU LEU MET SEQRES 6 A 519 LEU ASP GLY THR ASP TRP PRO VAL ALA PHE LEU GLY ALA SEQRES 7 A 519 ILE TYR ALA GLY ILE VAL PRO VAL ALA VAL ASN THR LEU SEQRES 8 A 519 LEU THR ALA ASP ASP TYR ALA TYR MET LEU GLU HIS SER SEQRES 9 A 519 ARG ALA GLN ALA VAL LEU VAL SER GLY ALA LEU HIS PRO SEQRES 10 A 519 VAL LEU LYS ALA ALA LEU THR LYS SER ASP HIS GLU VAL SEQRES 11 A 519 GLN ARG VAL ILE VAL SER ARG PRO ALA ALA PRO LEU GLU SEQRES 12 A 519 PRO GLY GLU VAL ASP PHE ALA GLU PHE VAL GLY ALA HIS SEQRES 13 A 519 ALA PRO LEU GLU LYS PRO ALA ALA THR GLN ALA ASP ASP SEQRES 14 A 519 PRO ALA PHE TRP LEU TYR SER SER GLY SER THR GLY ARG SEQRES 15 A 519 PRO LYS GLY VAL VAL HIS THR HIS ALA ASN PRO TYR TRP SEQRES 16 A 519 THR SER GLU LEU TYR GLY ARG ASN THR LEU HIS LEU ARG SEQRES 17 A 519 GLU ASP ASP VAL CYS PHE SER ALA ALA LYS LEU PHE PHE SEQRES 18 A 519 ALA TYR GLY LEU GLY ASN ALA LEU THR PHE PRO MET THR SEQRES 19 A 519 VAL GLY ALA THR THR LEU LEU MET GLY GLU ARG PRO THR SEQRES 20 A 519 PRO ASP ALA VAL PHE LYS ARG TRP LEU GLY GLY VAL GLY SEQRES 21 A 519 GLY VAL LYS PRO THR VAL PHE TYR GLY ALA PRO THR GLY SEQRES 22 A 519 TYR ALA GLY MET LEU ALA ALA PRO ASN LEU PRO SER ARG SEQRES 23 A 519 ASP GLN VAL ALA LEU ARG LEU ALA SER SER ALA GLY GLU SEQRES 24 A 519 ALA LEU PRO ALA GLU ILE GLY GLN ARG PHE GLN ARG HIS SEQRES 25 A 519 PHE GLY LEU ASP ILE VAL ASP GLY ILE GLY SER THR GLU SEQRES 26 A 519 MET LEU HIS ILE PHE LEU SER ASN LEU PRO ASP ARG VAL SEQRES 27 A 519 ARG TYR GLY THR THR GLY TRP PRO VAL PRO GLY TYR GLN SEQRES 28 A 519 ILE GLU LEU ARG GLY ASP GLY GLY GLY PRO VAL ALA ASP SEQRES 29 A 519 GLY GLU PRO GLY ASP LEU TYR ILE HIS GLY PRO SER SER SEQRES 30 A 519 ALA THR MET TYR TRP GLY ASN ARG ALA LYS SER ARG ASP SEQRES 31 A 519 THR PHE GLN GLY GLY TRP THR LYS SER GLY ASP LYS TYR SEQRES 32 A 519 VAL ARG ASN ASP ASP GLY SER TYR THR TYR ALA GLY ARG SEQRES 33 A 519 THR ASP ASP MET LEU LYS VAL SER GLY ILE TYR VAL SER SEQRES 34 A 519 PRO PHE GLU ILE GLU ALA THR LEU VAL GLN HIS PRO GLY SEQRES 35 A 519 VAL LEU GLU ALA ALA VAL VAL GLY VAL ALA ASP GLU HIS SEQRES 36 A 519 GLY LEU THR LYS PRO LYS ALA TYR VAL VAL PRO ARG PRO SEQRES 37 A 519 GLY GLN THR LEU SER GLU THR GLU LEU LYS THR PHE ILE SEQRES 38 A 519 LYS ASP ARG LEU ALA PRO TYR LYS TYR PRO ARG SER THR SEQRES 39 A 519 VAL PHE VAL ALA GLU LEU PRO LYS THR ALA THR GLY LYS SEQRES 40 A 519 ILE GLN ARG PHE LYS LEU ARG GLU GLY VAL LEU GLY SEQRES 1 B 519 VAL THR PRO PRO PRO GLU LYS PHE ASN PHE ALA GLU HIS SEQRES 2 B 519 LEU LEU GLN THR ASN ARG VAL ARG PRO ASP LYS THR ALA SEQRES 3 B 519 PHE VAL ASP ASP ILE SER SER LEU SER PHE ALA GLN LEU SEQRES 4 B 519 GLU ALA GLN THR ARG GLN LEU ALA ALA ALA LEU ARG ALA SEQRES 5 B 519 ILE GLY VAL LYS ARG GLU GLU ARG VAL LEU LEU LEU MET SEQRES 6 B 519 LEU ASP GLY THR ASP TRP PRO VAL ALA PHE LEU GLY ALA SEQRES 7 B 519 ILE TYR ALA GLY ILE VAL PRO VAL ALA VAL ASN THR LEU SEQRES 8 B 519 LEU THR ALA ASP ASP TYR ALA TYR MET LEU GLU HIS SER SEQRES 9 B 519 ARG ALA GLN ALA VAL LEU VAL SER GLY ALA LEU HIS PRO SEQRES 10 B 519 VAL LEU LYS ALA ALA LEU THR LYS SER ASP HIS GLU VAL SEQRES 11 B 519 GLN ARG VAL ILE VAL SER ARG PRO ALA ALA PRO LEU GLU SEQRES 12 B 519 PRO GLY GLU VAL ASP PHE ALA GLU PHE VAL GLY ALA HIS SEQRES 13 B 519 ALA PRO LEU GLU LYS PRO ALA ALA THR GLN ALA ASP ASP SEQRES 14 B 519 PRO ALA PHE TRP LEU TYR SER SER GLY SER THR GLY ARG SEQRES 15 B 519 PRO LYS GLY VAL VAL HIS THR HIS ALA ASN PRO TYR TRP SEQRES 16 B 519 THR SER GLU LEU TYR GLY ARG ASN THR LEU HIS LEU ARG SEQRES 17 B 519 GLU ASP ASP VAL CYS PHE SER ALA ALA LYS LEU PHE PHE SEQRES 18 B 519 ALA TYR GLY LEU GLY ASN ALA LEU THR PHE PRO MET THR SEQRES 19 B 519 VAL GLY ALA THR THR LEU LEU MET GLY GLU ARG PRO THR SEQRES 20 B 519 PRO ASP ALA VAL PHE LYS ARG TRP LEU GLY GLY VAL GLY SEQRES 21 B 519 GLY VAL LYS PRO THR VAL PHE TYR GLY ALA PRO THR GLY SEQRES 22 B 519 TYR ALA GLY MET LEU ALA ALA PRO ASN LEU PRO SER ARG SEQRES 23 B 519 ASP GLN VAL ALA LEU ARG LEU ALA SER SER ALA GLY GLU SEQRES 24 B 519 ALA LEU PRO ALA GLU ILE GLY GLN ARG PHE GLN ARG HIS SEQRES 25 B 519 PHE GLY LEU ASP ILE VAL ASP GLY ILE GLY SER THR GLU SEQRES 26 B 519 MET LEU HIS ILE PHE LEU SER ASN LEU PRO ASP ARG VAL SEQRES 27 B 519 ARG TYR GLY THR THR GLY TRP PRO VAL PRO GLY TYR GLN SEQRES 28 B 519 ILE GLU LEU ARG GLY ASP GLY GLY GLY PRO VAL ALA ASP SEQRES 29 B 519 GLY GLU PRO GLY ASP LEU TYR ILE HIS GLY PRO SER SER SEQRES 30 B 519 ALA THR MET TYR TRP GLY ASN ARG ALA LYS SER ARG ASP SEQRES 31 B 519 THR PHE GLN GLY GLY TRP THR LYS SER GLY ASP LYS TYR SEQRES 32 B 519 VAL ARG ASN ASP ASP GLY SER TYR THR TYR ALA GLY ARG SEQRES 33 B 519 THR ASP ASP MET LEU LYS VAL SER GLY ILE TYR VAL SER SEQRES 34 B 519 PRO PHE GLU ILE GLU ALA THR LEU VAL GLN HIS PRO GLY SEQRES 35 B 519 VAL LEU GLU ALA ALA VAL VAL GLY VAL ALA ASP GLU HIS SEQRES 36 B 519 GLY LEU THR LYS PRO LYS ALA TYR VAL VAL PRO ARG PRO SEQRES 37 B 519 GLY GLN THR LEU SER GLU THR GLU LEU LYS THR PHE ILE SEQRES 38 B 519 LYS ASP ARG LEU ALA PRO TYR LYS TYR PRO ARG SER THR SEQRES 39 B 519 VAL PHE VAL ALA GLU LEU PRO LYS THR ALA THR GLY LYS SEQRES 40 B 519 ILE GLN ARG PHE LYS LEU ARG GLU GLY VAL LEU GLY HET 3U4 A1000 10 HET 3U4 A1001 10 HET 3U4 B1000 10 HETNAM 3U4 2-FLUOROBENZOIC ACID FORMUL 3 3U4 3(C7 H5 F O2) FORMUL 6 HOH *738(H2 O) HELIX 1 1 ASN A 14 ASN A 23 1 10 HELIX 2 2 PHE A 41 ILE A 58 1 18 HELIX 3 3 THR A 74 ALA A 86 1 13 HELIX 4 4 THR A 98 ARG A 110 1 13 HELIX 5 5 LEU A 120 SER A 131 1 12 HELIX 6 6 PHE A 154 ALA A 160 1 7 HELIX 7 7 HIS A 195 TYR A 205 1 11 HELIX 8 8 PHE A 226 ALA A 233 1 8 HELIX 9 9 LEU A 234 GLY A 241 1 8 HELIX 10 10 THR A 252 LEU A 261 1 10 HELIX 11 11 ALA A 275 ALA A 284 1 10 HELIX 12 12 SER A 290 VAL A 294 5 5 HELIX 13 13 PRO A 307 GLY A 319 1 13 HELIX 14 14 ASN A 389 THR A 396 1 8 HELIX 15 15 SER A 434 VAL A 443 1 10 HELIX 16 16 SER A 478 LEU A 490 1 13 HELIX 17 17 ALA A 491 TYR A 495 5 5 HELIX 18 18 GLN A 514 GLU A 520 1 7 HELIX 19 19 ASN B 14 ASN B 23 1 10 HELIX 20 20 PHE B 41 ILE B 58 1 18 HELIX 21 21 THR B 74 ALA B 86 1 13 HELIX 22 22 THR B 98 ARG B 110 1 13 HELIX 23 23 LEU B 120 SER B 131 1 12 HELIX 24 24 PHE B 154 ALA B 160 1 7 HELIX 25 25 HIS B 195 TYR B 205 1 11 HELIX 26 26 PHE B 226 ALA B 233 1 8 HELIX 27 27 LEU B 234 GLY B 241 1 8 HELIX 28 28 THR B 252 LEU B 261 1 10 HELIX 29 29 ALA B 275 ALA B 285 1 11 HELIX 30 30 SER B 290 VAL B 294 5 5 HELIX 31 31 PRO B 307 GLY B 319 1 13 HELIX 32 32 ASN B 389 THR B 396 1 8 HELIX 33 33 SER B 434 VAL B 443 1 10 HELIX 34 34 SER B 478 LYS B 487 1 10 HELIX 35 35 ALA B 491 TYR B 495 5 5 HELIX 36 36 GLN B 514 GLY B 521 1 8 SHEET 1 A 9 SER A 38 SER A 40 0 SHEET 2 A 9 THR A 30 VAL A 33 -1 N PHE A 32 O LEU A 39 SHEET 3 A 9 THR A 243 LEU A 245 1 O THR A 244 N ALA A 31 SHEET 4 A 9 VAL A 217 SER A 220 1 N CYS A 218 O LEU A 245 SHEET 5 A 9 VAL A 271 GLY A 274 1 O VAL A 271 N PHE A 219 SHEET 6 A 9 LEU A 298 SER A 301 1 O SER A 300 N PHE A 272 SHEET 7 A 9 ILE A 322 GLY A 327 1 O VAL A 323 N ALA A 299 SHEET 8 A 9 ILE A 334 SER A 337 -1 O LEU A 336 N ILE A 326 SHEET 9 A 9 TRP A 350 PRO A 351 -1 O TRP A 350 N SER A 337 SHEET 1 B 7 VAL A 152 ASP A 153 0 SHEET 2 B 7 ARG A 137 SER A 141 1 N VAL A 140 O VAL A 152 SHEET 3 B 7 ALA A 113 SER A 117 1 N VAL A 116 O SER A 141 SHEET 4 B 7 ARG A 65 LEU A 69 1 N LEU A 67 O LEU A 115 SHEET 5 B 7 VAL A 89 ALA A 92 1 O VAL A 91 N LEU A 68 SHEET 6 B 7 PRO A 175 SER A 181 1 O TRP A 178 N ALA A 92 SHEET 7 B 7 LYS A 189 THR A 194 -1 O HIS A 193 N ALA A 176 SHEET 1 C 4 GLN A 356 ARG A 360 0 SHEET 2 C 4 PRO A 372 HIS A 378 -1 O ASP A 374 N ARG A 360 SHEET 3 C 4 TRP A 401 ARG A 410 -1 O ASP A 406 N LEU A 375 SHEET 4 C 4 PHE A 397 GLN A 398 -1 N GLN A 398 O TRP A 401 SHEET 1 D 4 GLN A 356 ARG A 360 0 SHEET 2 D 4 PRO A 372 HIS A 378 -1 O ASP A 374 N ARG A 360 SHEET 3 D 4 TRP A 401 ARG A 410 -1 O ASP A 406 N LEU A 375 SHEET 4 D 4 TYR A 416 ARG A 421 -1 O ALA A 419 N LYS A 407 SHEET 1 E 2 LEU A 426 VAL A 428 0 SHEET 2 E 2 ILE A 431 VAL A 433 -1 O VAL A 433 N LEU A 426 SHEET 1 F 3 VAL A 448 ALA A 457 0 SHEET 2 F 3 THR A 463 PRO A 471 -1 O VAL A 470 N LEU A 449 SHEET 3 F 3 SER A 498 PHE A 501 1 O VAL A 500 N ALA A 467 SHEET 1 G 9 SER B 38 SER B 40 0 SHEET 2 G 9 THR B 30 VAL B 33 -1 N ALA B 31 O LEU B 39 SHEET 3 G 9 THR B 243 LEU B 245 1 O THR B 244 N VAL B 33 SHEET 4 G 9 VAL B 217 SER B 220 1 N CYS B 218 O THR B 243 SHEET 5 G 9 VAL B 271 GLY B 274 1 O VAL B 271 N PHE B 219 SHEET 6 G 9 LEU B 298 SER B 301 1 O SER B 300 N PHE B 272 SHEET 7 G 9 ILE B 322 GLY B 327 1 O VAL B 323 N ALA B 299 SHEET 8 G 9 ILE B 334 SER B 337 -1 O LEU B 336 N ILE B 326 SHEET 9 G 9 TRP B 350 PRO B 351 -1 O TRP B 350 N SER B 337 SHEET 1 H 7 GLU B 151 ASP B 153 0 SHEET 2 H 7 ARG B 137 SER B 141 1 N VAL B 140 O VAL B 152 SHEET 3 H 7 ALA B 113 SER B 117 1 N VAL B 114 O ILE B 139 SHEET 4 H 7 ARG B 65 LEU B 69 1 N LEU B 67 O LEU B 115 SHEET 5 H 7 VAL B 89 ALA B 92 1 O VAL B 91 N LEU B 68 SHEET 6 H 7 PRO B 175 SER B 181 1 O TRP B 178 N PRO B 90 SHEET 7 H 7 LYS B 189 THR B 194 -1 O HIS B 193 N ALA B 176 SHEET 1 I 4 GLN B 356 ARG B 360 0 SHEET 2 I 4 PRO B 372 HIS B 378 -1 O HIS B 378 N GLN B 356 SHEET 3 I 4 TRP B 401 ARG B 410 -1 O THR B 402 N ILE B 377 SHEET 4 I 4 PHE B 397 GLN B 398 -1 N GLN B 398 O TRP B 401 SHEET 1 J 4 GLN B 356 ARG B 360 0 SHEET 2 J 4 PRO B 372 HIS B 378 -1 O HIS B 378 N GLN B 356 SHEET 3 J 4 TRP B 401 ARG B 410 -1 O THR B 402 N ILE B 377 SHEET 4 J 4 TYR B 416 ARG B 421 -1 O GLY B 420 N LYS B 407 SHEET 1 K 2 LEU B 426 VAL B 428 0 SHEET 2 K 2 ILE B 431 VAL B 433 -1 O ILE B 431 N VAL B 428 SHEET 1 L 3 VAL B 448 ALA B 457 0 SHEET 2 L 3 THR B 463 PRO B 471 -1 O LYS B 464 N VAL B 456 SHEET 3 L 3 SER B 498 PHE B 501 1 O VAL B 500 N ALA B 467 SITE 1 AC1 11 ALA A 227 TYR A 228 ALA A 302 GLY A 303 SITE 2 AC1 11 ILE A 326 GLY A 327 SER A 328 LEU A 332 SITE 3 AC1 11 LYS A 427 HOH A1123 HOH A1185 SITE 1 AC2 8 ALA A 221 PHE A 272 GLY A 274 ALA A 275 SITE 2 AC2 8 GLY A 278 MET A 282 HOH A1398 HOH A1438 SITE 1 AC3 12 ALA B 227 TYR B 228 ALA B 302 GLY B 303 SITE 2 AC3 12 ILE B 326 GLY B 327 SER B 328 LEU B 332 SITE 3 AC3 12 HIS B 333 LYS B 427 HOH B1168 HOH B1247 CRYST1 58.885 95.749 98.605 90.00 110.43 90.00 P 1 21 1 4 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 0.016982 0.000000 0.006325 0.00000 SCALE2 0.000000 0.010444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010822 0.00000