HEADER LIGASE 14-DEC-11 3VMM TITLE CRYSTAL STRUCTURE OF BACD, AN L-AMINO ACID DIPEPTIDE LIGASE FROM TITLE 2 BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANINE-ANTICAPSIN LIGASE BACD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BACILYSIN SYNTHETASE, L-AMINO ACID LIGASE; COMPND 5 EC: 6.3.2.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: BACD, BSU37710, IPA-83D; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ATP-GRASP DOMAIN, AMINO ACID LIGASE, ATP BINDING, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHOMURA,Y.HIGUCHI REVDAT 2 20-MAR-24 3VMM 1 REMARK SEQADV LINK REVDAT 1 11-APR-12 3VMM 0 JRNL AUTH Y.SHOMURA,E.HINOKUCHI,H.IKEDA,A.SENOO,Y.TAKAHASHI,J.SAITO, JRNL AUTH 2 H.KOMORI,N.SHIBATA,Y.YONETANI,Y.HIGUCHI JRNL TITL STRUCTURAL AND ENZYMATIC CHARACTERIZATION OF BACD, AN JRNL TITL 2 L-AMINO ACID DIPEPTIDE LIGASE FROM BACILLUS SUBTILIS JRNL REF PROTEIN SCI. 2012 JRNL REFN ESSN 1469-896X JRNL PMID 22407814 JRNL DOI 10.1002/PRO.2058 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 24770 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1327 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1755 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3675 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.04000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.232 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.920 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3804 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5166 ; 1.297 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 470 ; 5.956 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;39.076 ;25.523 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 645 ;17.771 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.692 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 576 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2870 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2354 ; 0.336 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3792 ; 0.694 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1450 ; 1.263 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1374 ; 2.173 ; 4.500 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 472 REMARK 3 RESIDUE RANGE : A 501 A 504 REMARK 3 RESIDUE RANGE : A 601 A 747 REMARK 3 ORIGIN FOR THE GROUP (A): -1.2620 -46.1950 -9.8030 REMARK 3 T TENSOR REMARK 3 T11: 0.1408 T22: 0.0546 REMARK 3 T33: 0.2168 T12: 0.0041 REMARK 3 T13: -0.1254 T23: -0.0189 REMARK 3 L TENSOR REMARK 3 L11: 1.7772 L22: 2.0765 REMARK 3 L33: 0.7530 L12: -0.9044 REMARK 3 L13: 0.3995 L23: -0.5482 REMARK 3 S TENSOR REMARK 3 S11: -0.2051 S12: -0.0723 S13: 0.4367 REMARK 3 S21: 0.3005 S22: 0.0358 S23: -0.5227 REMARK 3 S31: -0.0506 S32: -0.0034 S33: 0.1692 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3VMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000095234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.900 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26252 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 1.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.48700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS PROPANE, 60MM SODIUM REMARK 280 CITRATE, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 98.49467 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 49.24733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.87100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.62367 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 123.11833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 98.49467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 49.24733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 24.62367 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 73.87100 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 123.11833 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: MONOMERIC 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 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 -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 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 OE1 GLU A 324 O HOH A 721 2.18 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 ASP A 11 -168.00 -162.61 REMARK 500 HIS A 78 46.81 -90.94 REMARK 500 LYS A 151 118.13 -36.95 REMARK 500 THR A 159 -54.30 -121.73 REMARK 500 GLU A 170 -70.59 -66.93 REMARK 500 LEU A 182 -152.34 -104.01 REMARK 500 TYR A 242 -151.97 -104.06 REMARK 500 ASP A 254 53.24 32.44 REMARK 500 ILE A 260 -59.81 -120.03 REMARK 500 GLN A 304 -61.61 -101.08 REMARK 500 ALA A 327 37.57 -87.72 REMARK 500 TRP A 332 -146.74 55.46 REMARK 500 TYR A 372 -178.55 -178.94 REMARK 500 ASP A 396 66.82 37.08 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 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 109 OE2 REMARK 620 2 LEU A 182 O 94.0 REMARK 620 3 GLU A 324 OE1 122.1 133.0 REMARK 620 4 ADP A 503 O3B 169.3 81.0 57.9 REMARK 620 5 P0D A 504 O3P 130.2 119.4 60.7 60.1 REMARK 620 6 HOH A 721 O 78.6 172.7 52.8 106.2 66.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 311 OE1 REMARK 620 2 GLU A 324 OE2 78.8 REMARK 620 3 ADP A 503 O1B 161.9 106.7 REMARK 620 4 ADP A 503 O1A 88.9 68.7 77.5 REMARK 620 5 P0D A 504 O5P 95.0 121.0 96.7 170.1 REMARK 620 6 HOH A 719 O 79.2 142.6 86.8 81.1 90.7 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 MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P0D A 504 DBREF 3VMM A 1 472 UNP P39641 BACD_BACSU 1 472 SEQADV 3VMM GLY A -1 UNP P39641 EXPRESSION TAG SEQADV 3VMM ALA A 0 UNP P39641 EXPRESSION TAG SEQRES 1 A 474 GLY ALA MET GLU ARG LYS THR VAL LEU VAL ILE ALA ASP SEQRES 2 A 474 LEU GLY GLY CYS PRO PRO HIS MET PHE TYR LYS SER ALA SEQRES 3 A 474 ALA GLU LYS TYR ASN LEU VAL SER PHE ILE PRO ARG PRO SEQRES 4 A 474 PHE ALA ILE THR ALA SER HIS ALA ALA LEU ILE GLU LYS SEQRES 5 A 474 TYR SER VAL ALA VAL ILE LYS ASP LYS ASP TYR PHE LYS SEQRES 6 A 474 SER LEU ALA ASP PHE GLU HIS PRO ASP SER ILE TYR TRP SEQRES 7 A 474 ALA HIS GLU ASP HIS ASN LYS PRO GLU GLU GLU VAL VAL SEQRES 8 A 474 GLU GLN ILE VAL LYS VAL ALA GLU MET PHE GLY ALA ASP SEQRES 9 A 474 ALA ILE THR THR ASN ASN GLU LEU PHE ILE ALA PRO MET SEQRES 10 A 474 ALA LYS ALA CYS GLU ARG LEU GLY LEU ARG GLY ALA GLY SEQRES 11 A 474 VAL GLN ALA ALA GLU ASN ALA ARG ASP LYS ASN LYS MET SEQRES 12 A 474 ARG ASP ALA PHE ASN LYS ALA GLY VAL LYS SER ILE LYS SEQRES 13 A 474 ASN LYS ARG VAL THR THR LEU GLU ASP PHE ARG ALA ALA SEQRES 14 A 474 LEU GLU GLU ILE GLY THR PRO LEU ILE LEU LYS PRO THR SEQRES 15 A 474 TYR LEU ALA SER SER ILE GLY VAL THR LEU ILE THR ASP SEQRES 16 A 474 THR GLU THR ALA GLU ASP GLU PHE ASN ARG VAL ASN ASP SEQRES 17 A 474 TYR LEU LYS SER ILE ASN VAL PRO LYS ALA VAL THR PHE SEQRES 18 A 474 GLU ALA PRO PHE ILE ALA GLU GLU PHE LEU GLN GLY GLU SEQRES 19 A 474 TYR GLY ASP TRP TYR GLN THR GLU GLY TYR SER ASP TYR SEQRES 20 A 474 ILE SER ILE GLU GLY ILE MET ALA ASP GLY GLU TYR PHE SEQRES 21 A 474 PRO ILE ALA ILE HIS ASP LYS THR PRO GLN ILE GLY PHE SEQRES 22 A 474 THR GLU THR SER HIS ILE THR PRO SER ILE LEU ASP GLU SEQRES 23 A 474 GLU ALA LYS LYS LYS ILE VAL GLU ALA ALA LYS LYS ALA SEQRES 24 A 474 ASN GLU GLY LEU GLY LEU GLN ASN CYS ALA THR HIS THR SEQRES 25 A 474 GLU ILE LYS LEU MET LYS ASN ARG GLU PRO GLY LEU ILE SEQRES 26 A 474 GLU SER ALA ALA ARG PHE ALA GLY TRP ASN MET ILE PRO SEQRES 27 A 474 ASN ILE LYS LYS VAL PHE GLY LEU ASP MET ALA GLN LEU SEQRES 28 A 474 LEU LEU ASP VAL LEU CYS PHE GLY LYS ASP ALA ASP LEU SEQRES 29 A 474 PRO ASP GLY LEU LEU ASP GLN GLU PRO TYR TYR VAL ALA SEQRES 30 A 474 ASP CYS HIS LEU TYR PRO GLN HIS PHE LYS GLN ASN GLY SEQRES 31 A 474 GLN ILE PRO GLU THR ALA GLU ASP LEU VAL ILE GLU ALA SEQRES 32 A 474 ILE ASP ILE PRO ASP GLY LEU LEU LYS GLY ASP THR GLU SEQRES 33 A 474 ILE VAL SER PHE SER ALA ALA ALA PRO GLY THR SER VAL SEQRES 34 A 474 ASP LEU THR LEU PHE GLU ALA PHE ASN SER ILE ALA ALA SEQRES 35 A 474 PHE GLU LEU LYS GLY SER ASN SER GLN ASP VAL ALA GLU SEQRES 36 A 474 SER ILE ARG GLN ILE GLN GLN HIS ALA LYS LEU THR ALA SEQRES 37 A 474 LYS TYR VAL LEU PRO VAL HET MG A 501 1 HET MG A 502 1 HET ADP A 503 27 HET P0D A 504 22 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM P0D (2S)-3-[(S)-[(1R)-1-AMINOETHYL](PHOSPHONOOXY) HETNAM 2 P0D PHOSPHORYL]-2-BENZYLPROPANOIC ACID FORMUL 2 MG 2(MG 2+) FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 P0D C12 H19 N O7 P2 FORMUL 6 HOH *147(H2 O) HELIX 1 1 PRO A 16 GLU A 26 1 11 HELIX 2 2 ARG A 36 ILE A 40 5 5 HELIX 3 3 THR A 41 TYR A 51 1 11 HELIX 4 4 LYS A 59 PHE A 62 5 4 HELIX 5 5 SER A 64 GLU A 69 5 6 HELIX 6 6 PRO A 84 PHE A 99 1 16 HELIX 7 7 ASN A 108 LEU A 110 5 3 HELIX 8 8 PHE A 111 LEU A 122 1 12 HELIX 9 9 GLY A 128 ALA A 135 1 8 HELIX 10 10 ASP A 137 ALA A 148 1 12 HELIX 11 11 THR A 160 ILE A 171 1 12 HELIX 12 12 THR A 196 LYS A 209 1 14 HELIX 13 13 GLU A 232 TYR A 237 1 6 HELIX 14 14 ASP A 283 GLY A 302 1 20 HELIX 15 15 LYS A 316 ARG A 318 5 3 HELIX 16 16 ASN A 333 GLY A 343 1 11 HELIX 17 17 ASP A 345 GLY A 357 1 13 HELIX 18 18 LYS A 358 ALA A 360 5 3 HELIX 19 19 TYR A 380 ASN A 387 1 8 HELIX 20 20 PHE A 432 ASN A 436 5 5 HELIX 21 21 ASN A 447 ALA A 462 1 16 SHEET 1 A 4 SER A 52 LYS A 57 0 SHEET 2 A 4 TYR A 28 ILE A 34 1 N SER A 32 O ILE A 56 SHEET 3 A 4 LYS A 4 ILE A 9 1 N VAL A 8 O PHE A 33 SHEET 4 A 4 ALA A 103 THR A 106 1 O ALA A 103 N LEU A 7 SHEET 1 B 4 ASN A 155 VAL A 158 0 SHEET 2 B 4 PHE A 223 GLU A 227 -1 O PHE A 223 N VAL A 158 SHEET 3 B 4 LEU A 175 PRO A 179 -1 N ILE A 176 O GLU A 226 SHEET 4 B 4 THR A 189 ILE A 191 -1 O THR A 189 N LEU A 177 SHEET 1 C 8 GLU A 319 ALA A 326 0 SHEET 2 C 8 CYS A 306 MET A 315 -1 N LYS A 313 O GLY A 321 SHEET 3 C 8 TYR A 245 ALA A 253 -1 N MET A 252 O CYS A 306 SHEET 4 C 8 GLU A 256 LYS A 265 -1 O ALA A 261 N GLU A 249 SHEET 5 C 8 SER A 275 THR A 278 -1 O ILE A 277 N ASP A 264 SHEET 6 C 8 TYR A 373 LEU A 379 -1 O VAL A 374 N THR A 278 SHEET 7 C 8 ALA A 439 GLY A 445 -1 O GLY A 445 N TYR A 373 SHEET 8 C 8 GLU A 414 ALA A 420 -1 N SER A 419 O ALA A 440 SHEET 1 D 3 THR A 425 VAL A 427 0 SHEET 2 D 3 GLU A 395 ASP A 403 -1 N LEU A 397 O VAL A 427 SHEET 3 D 3 LYS A 463 VAL A 469 -1 O LYS A 467 N VAL A 398 LINK OE2 GLU A 109 MG MG A 502 1555 1555 2.73 LINK O LEU A 182 MG MG A 502 1555 1555 2.90 LINK OE1 GLU A 311 MG MG A 501 1555 1555 2.06 LINK OE2 GLU A 324 MG MG A 501 1555 1555 2.01 LINK OE1 GLU A 324 MG MG A 502 1555 1555 2.37 LINK MG MG A 501 O1B ADP A 503 1555 1555 2.02 LINK MG MG A 501 O1A ADP A 503 1555 1555 2.20 LINK MG MG A 501 O5P P0D A 504 1555 1555 2.03 LINK MG MG A 501 O HOH A 719 1555 1555 2.25 LINK MG MG A 502 O3B ADP A 503 1555 1555 2.60 LINK MG MG A 502 O3P P0D A 504 1555 1555 2.82 LINK MG MG A 502 O HOH A 721 1555 1555 2.52 CISPEP 1 THR A 173 PRO A 174 0 -5.57 CISPEP 2 THR A 278 PRO A 279 0 -9.84 SITE 1 AC1 5 GLU A 311 GLU A 324 ADP A 503 P0D A 504 SITE 2 AC1 5 HOH A 719 SITE 1 AC2 8 GLU A 109 LYS A 138 LEU A 182 ALA A 183 SITE 2 AC2 8 GLU A 324 ADP A 503 P0D A 504 HOH A 721 SITE 1 AC3 24 LYS A 138 ILE A 176 LYS A 178 LEU A 182 SITE 2 AC3 24 ALA A 183 SER A 184 SER A 185 VAL A 188 SITE 3 AC3 24 GLU A 226 GLU A 227 PHE A 228 LEU A 229 SITE 4 AC3 24 GLN A 268 PHE A 271 GLU A 311 ILE A 323 SITE 5 AC3 24 GLU A 324 MG A 501 MG A 502 P0D A 504 SITE 6 AC3 24 HOH A 631 HOH A 685 HOH A 706 HOH A 719 SITE 1 AC4 19 LEU A 12 GLY A 13 GLY A 14 ALA A 183 SITE 2 AC4 19 SER A 184 GLU A 273 HIS A 309 GLU A 311 SITE 3 AC4 19 GLU A 324 ARG A 328 GLY A 331 MG A 501 SITE 4 AC4 19 MG A 502 ADP A 503 HOH A 650 HOH A 719 SITE 5 AC4 19 HOH A 721 HOH A 744 HOH A 745 CRYST1 130.787 130.787 147.742 90.00 90.00 120.00 P 65 2 2 12 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 0.007646 0.004414 0.000000 0.00000 SCALE2 0.000000 0.008829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006769 0.00000