HEADER LIGASE 19-DEC-13 3WNZ TITLE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS YWFE, AN L-AMINO ACID LIGASE, TITLE 2 WITH BOUND ADP-MG-PI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANINE-ANTICAPSIN LIGASE BACD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 4-468; COMPND 5 SYNONYM: BACILYSIN SYNTHETASE, L-AMINO ACID LIGASE; COMPND 6 EC: 6.3.2.28; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YWFE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ARCTICEXPRESS RIL (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS ATP-GRASP FOLD, LIGASE, ATP BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.TSUDA,S.KOJIMA REVDAT 2 20-MAR-24 3WNZ 1 REMARK SEQADV LINK REVDAT 1 14-MAY-14 3WNZ 0 JRNL AUTH T.TSUDA,M.ASAMI,Y.KOGUCHI,S.KOJIMA JRNL TITL SINGLE MUTATION ALTERS THE SUBSTRATE SPECIFICITY OF L-AMINO JRNL TITL 2 ACID LIGASE JRNL REF BIOCHEMISTRY V. 53 2650 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24702628 JRNL DOI 10.1021/BI500292B REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 41606 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2232 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3213 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3626 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 396 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.24000 REMARK 3 B22 (A**2) : -1.24000 REMARK 3 B33 (A**2) : 4.01000 REMARK 3 B12 (A**2) : -1.24000 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): 0.158 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.238 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3736 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3527 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5071 ; 1.342 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8161 ; 0.704 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 464 ; 7.477 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;39.496 ;25.588 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;14.923 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;24.865 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4219 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 801 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 125 REMARK 3 ORIGIN FOR THE GROUP (A): 9.9816 4.5601 42.9114 REMARK 3 T TENSOR REMARK 3 T11: 0.2322 T22: 0.1930 REMARK 3 T33: 0.2105 T12: -0.0243 REMARK 3 T13: 0.1645 T23: 0.1098 REMARK 3 L TENSOR REMARK 3 L11: 1.6372 L22: 1.5495 REMARK 3 L33: 0.7361 L12: 0.3277 REMARK 3 L13: -0.0002 L23: -0.2672 REMARK 3 S TENSOR REMARK 3 S11: 0.1971 S12: -0.0982 S13: 0.1460 REMARK 3 S21: 0.2258 S22: -0.1522 S23: 0.0814 REMARK 3 S31: 0.0669 S32: -0.0418 S33: -0.0450 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 126 A 149 REMARK 3 ORIGIN FOR THE GROUP (A): 32.6671 11.2282 40.8886 REMARK 3 T TENSOR REMARK 3 T11: 0.1736 T22: 0.1900 REMARK 3 T33: 0.3129 T12: -0.0234 REMARK 3 T13: 0.0482 T23: 0.2297 REMARK 3 L TENSOR REMARK 3 L11: 3.0726 L22: 5.7928 REMARK 3 L33: 2.4045 L12: 2.2521 REMARK 3 L13: 0.1146 L23: 1.0379 REMARK 3 S TENSOR REMARK 3 S11: 0.2647 S12: -0.1272 S13: -0.0242 REMARK 3 S21: 0.3504 S22: -0.5497 S23: -0.5376 REMARK 3 S31: -0.0089 S32: 0.2541 S33: 0.2850 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 150 A 240 REMARK 3 ORIGIN FOR THE GROUP (A): 31.9279 24.5483 49.9612 REMARK 3 T TENSOR REMARK 3 T11: 0.3538 T22: 0.2314 REMARK 3 T33: 0.3535 T12: -0.1020 REMARK 3 T13: 0.0799 T23: 0.1105 REMARK 3 L TENSOR REMARK 3 L11: 0.6995 L22: 1.5355 REMARK 3 L33: 0.7362 L12: -0.6964 REMARK 3 L13: -0.0533 L23: -0.2922 REMARK 3 S TENSOR REMARK 3 S11: 0.0035 S12: -0.1284 S13: 0.2823 REMARK 3 S21: 0.5192 S22: -0.0565 S23: -0.1919 REMARK 3 S31: -0.2190 S32: 0.0651 S33: 0.0529 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 241 A 468 REMARK 3 ORIGIN FOR THE GROUP (A): 16.6054 26.7600 33.5079 REMARK 3 T TENSOR REMARK 3 T11: 0.1880 T22: 0.1534 REMARK 3 T33: 0.4229 T12: 0.0226 REMARK 3 T13: 0.2101 T23: 0.1507 REMARK 3 L TENSOR REMARK 3 L11: 1.7494 L22: 1.9199 REMARK 3 L33: 0.2165 L12: 1.4666 REMARK 3 L13: -0.1651 L23: -0.3299 REMARK 3 S TENSOR REMARK 3 S11: 0.2827 S12: 0.0033 S13: 0.6071 REMARK 3 S21: 0.2032 S22: -0.1972 S23: 0.3587 REMARK 3 S31: -0.0187 S32: 0.0080 S33: -0.0855 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 3WNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000096574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-12 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43922 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 88.9 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.31200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CRANK REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.3M NACL, 0.1M HEPES REMARK 280 -NAOH, 5% ETHYLENE GLYCOL, 1MM DTT, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 168.43600 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 84.21800 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 126.32700 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 42.10900 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 210.54500 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 168.43600 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 84.21800 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 42.10900 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 126.32700 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 210.54500 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: 4650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 84.21800 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 PRO A 0 REMARK 465 LEU A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 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 ND2 ASN A 387 O GLN A 460 2.06 REMARK 500 O HOH A 1306 O HOH A 1307 2.13 REMARK 500 O HOH A 1323 O HOH A 1324 2.14 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 -159.69 -158.77 REMARK 500 TYR A 61 56.13 -100.70 REMARK 500 LEU A 182 -148.19 -107.20 REMARK 500 TYR A 242 -154.88 -112.14 REMARK 500 ASP A 244 35.09 -95.30 REMARK 500 GLN A 304 -60.52 -105.08 REMARK 500 ALA A 327 41.33 -92.26 REMARK 500 TRP A 332 -144.74 46.17 REMARK 500 TYR A 372 168.52 176.67 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 311 OE1 REMARK 620 2 GLU A 324 OE1 81.1 REMARK 620 3 ADP A 501 O1A 98.2 90.0 REMARK 620 4 ADP A 501 O3B 176.9 101.5 80.3 REMARK 620 5 PO4 A 504 O1 97.2 95.0 164.4 84.3 REMARK 620 6 HOH A1001 O 91.5 172.5 89.7 85.8 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 324 OE1 REMARK 620 2 GLU A 324 OE2 59.1 REMARK 620 3 ADP A 501 O2B 97.1 84.0 REMARK 620 4 PO4 A 504 O2 93.7 150.7 112.1 REMARK 620 5 HOH A1002 O 83.0 83.6 165.4 82.4 REMARK 620 6 HOH A1248 O 157.7 99.3 85.1 106.2 89.4 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 ADP 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 MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VMM RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH PHOSPHINOPHOSPHATE ANALOG REMARK 900 RELATED ID: 3WO0 RELATED DB: PDB REMARK 900 RELATED ID: 3WO1 RELATED DB: PDB DBREF 3WNZ A 4 468 UNP P39641 BACD_BACSU 4 468 SEQADV 3WNZ GLY A -1 UNP P39641 EXPRESSION TAG SEQADV 3WNZ PRO A 0 UNP P39641 EXPRESSION TAG SEQADV 3WNZ LEU A 1 UNP P39641 EXPRESSION TAG SEQADV 3WNZ GLY A 2 UNP P39641 EXPRESSION TAG SEQADV 3WNZ SER A 3 UNP P39641 EXPRESSION TAG SEQRES 1 A 470 GLY PRO LEU GLY SER LYS THR VAL LEU VAL ILE ALA ASP SEQRES 2 A 470 LEU GLY GLY CYS PRO PRO HIS MET PHE TYR LYS SER ALA SEQRES 3 A 470 ALA GLU LYS TYR ASN LEU VAL SER PHE ILE PRO ARG PRO SEQRES 4 A 470 PHE ALA ILE THR ALA SER HIS ALA ALA LEU ILE GLU LYS SEQRES 5 A 470 TYR SER VAL ALA VAL ILE LYS ASP LYS ASP TYR PHE LYS SEQRES 6 A 470 SER LEU ALA ASP PHE GLU HIS PRO ASP SER ILE TYR TRP SEQRES 7 A 470 ALA HIS GLU ASP HIS ASN LYS PRO GLU GLU GLU VAL VAL SEQRES 8 A 470 GLU GLN ILE VAL LYS VAL ALA GLU MET PHE GLY ALA ASP SEQRES 9 A 470 ALA ILE THR THR ASN ASN GLU LEU PHE ILE ALA PRO MET SEQRES 10 A 470 ALA LYS ALA CYS GLU ARG LEU GLY LEU ARG GLY ALA GLY SEQRES 11 A 470 VAL GLN ALA ALA GLU ASN ALA ARG ASP LYS ASN LYS MET SEQRES 12 A 470 ARG ASP ALA PHE ASN LYS ALA GLY VAL LYS SER ILE LYS SEQRES 13 A 470 ASN LYS ARG VAL THR THR LEU GLU ASP PHE ARG ALA ALA SEQRES 14 A 470 LEU GLU GLU ILE GLY THR PRO LEU ILE LEU LYS PRO THR SEQRES 15 A 470 TYR LEU ALA SER SER ILE GLY VAL THR LEU ILE THR ASP SEQRES 16 A 470 THR GLU THR ALA GLU ASP GLU PHE ASN ARG VAL ASN ASP SEQRES 17 A 470 TYR LEU LYS SER ILE ASN VAL PRO LYS ALA VAL THR PHE SEQRES 18 A 470 GLU ALA PRO PHE ILE ALA GLU GLU PHE LEU GLN GLY GLU SEQRES 19 A 470 TYR GLY ASP TRP TYR GLN THR GLU GLY TYR SER ASP TYR SEQRES 20 A 470 ILE SER ILE GLU GLY ILE MET ALA ASP GLY GLU TYR PHE SEQRES 21 A 470 PRO ILE ALA ILE HIS ASP LYS THR PRO GLN ILE GLY PHE SEQRES 22 A 470 THR GLU THR SER HIS ILE THR PRO SER ILE LEU ASP GLU SEQRES 23 A 470 GLU ALA LYS LYS LYS ILE VAL GLU ALA ALA LYS LYS ALA SEQRES 24 A 470 ASN GLU GLY LEU GLY LEU GLN ASN CYS ALA THR HIS THR SEQRES 25 A 470 GLU ILE LYS LEU MET LYS ASN ARG GLU PRO GLY LEU ILE SEQRES 26 A 470 GLU SER ALA ALA ARG PHE ALA GLY TRP ASN MET ILE PRO SEQRES 27 A 470 ASN ILE LYS LYS VAL PHE GLY LEU ASP MET ALA GLN LEU SEQRES 28 A 470 LEU LEU ASP VAL LEU CYS PHE GLY LYS ASP ALA ASP LEU SEQRES 29 A 470 PRO ASP GLY LEU LEU ASP GLN GLU PRO TYR TYR VAL ALA SEQRES 30 A 470 ASP CYS HIS LEU TYR PRO GLN HIS PHE LYS GLN ASN GLY SEQRES 31 A 470 GLN ILE PRO GLU THR ALA GLU ASP LEU VAL ILE GLU ALA SEQRES 32 A 470 ILE ASP ILE PRO ASP GLY LEU LEU LYS GLY ASP THR GLU SEQRES 33 A 470 ILE VAL SER PHE SER ALA ALA ALA PRO GLY THR SER VAL SEQRES 34 A 470 ASP LEU THR LEU PHE GLU ALA PHE ASN SER ILE ALA ALA SEQRES 35 A 470 PHE GLU LEU LYS GLY SER ASN SER GLN ASP VAL ALA GLU SEQRES 36 A 470 SER ILE ARG GLN ILE GLN GLN HIS ALA LYS LEU THR ALA SEQRES 37 A 470 LYS TYR HET ADP A 501 27 HET MG A 502 1 HET MG A 503 1 HET PO4 A 504 5 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG 2(MG 2+) FORMUL 5 PO4 O4 P 3- FORMUL 6 HOH *396(H2 O) HELIX 1 1 PRO A 16 TYR A 28 1 13 HELIX 2 2 ARG A 36 ILE A 40 5 5 HELIX 3 3 THR A 41 SER A 52 1 12 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 GLY A 100 1 17 HELIX 7 7 ASN A 108 LEU A 110 5 3 HELIX 8 8 PHE A 111 GLY A 123 1 13 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 GLY A 172 1 13 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 ALA A 54 LYS A 57 0 SHEET 2 A 4 ASN A 29 ILE A 34 1 N ILE A 34 O ILE A 56 SHEET 3 A 4 THR A 5 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 ALA A 225 N LYS A 156 SHEET 3 B 4 LEU A 175 PRO A 179 -1 N LYS A 178 O ILE A 224 SHEET 4 B 4 THR A 189 ILE A 191 -1 O ILE A 191 N LEU A 175 SHEET 1 C 8 GLU A 319 ALA A 326 0 SHEET 2 C 8 CYS A 306 MET A 315 -1 N GLU A 311 O GLU A 324 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 GLU A 414 O LYS A 444 SHEET 1 D 3 SER A 426 ASP A 428 0 SHEET 2 D 3 ASP A 396 ASP A 403 -1 N LEU A 397 O VAL A 427 SHEET 3 D 3 LYS A 463 LYS A 467 -1 O LYS A 463 N ASP A 403 LINK OE1 GLU A 311 MG MG A 502 1555 1555 2.10 LINK OE1 GLU A 324 MG MG A 502 1555 1555 1.93 LINK OE1 GLU A 324 MG MG A 503 1555 1555 2.17 LINK OE2 GLU A 324 MG MG A 503 1555 1555 2.36 LINK O1A ADP A 501 MG MG A 502 1555 1555 2.15 LINK O3B ADP A 501 MG MG A 502 1555 1555 2.31 LINK O2B ADP A 501 MG MG A 503 1555 1555 1.89 LINK MG MG A 502 O1 PO4 A 504 1555 1555 1.87 LINK MG MG A 502 O HOH A1001 1555 1555 2.32 LINK MG MG A 503 O2 PO4 A 504 1555 1555 1.84 LINK MG MG A 503 O HOH A1002 1555 1555 1.93 LINK MG MG A 503 O HOH A1248 1555 1555 2.41 CISPEP 1 THR A 173 PRO A 174 0 -2.27 CISPEP 2 THR A 278 PRO A 279 0 -15.96 SITE 1 AC1 24 LYS A 138 ILE A 176 LYS A 178 ALA A 183 SITE 2 AC1 24 SER A 184 SER A 185 VAL A 188 GLU A 226 SITE 3 AC1 24 GLU A 227 PHE A 228 LEU A 229 GLN A 268 SITE 4 AC1 24 PHE A 271 GLU A 311 GLU A 324 MG A 502 SITE 5 AC1 24 MG A 503 PO4 A 504 HOH A1001 HOH A1150 SITE 6 AC1 24 HOH A1186 HOH A1205 HOH A1248 HOH A1320 SITE 1 AC2 6 GLU A 311 GLU A 324 ADP A 501 MG A 503 SITE 2 AC2 6 PO4 A 504 HOH A1001 SITE 1 AC3 6 GLU A 324 ADP A 501 MG A 502 PO4 A 504 SITE 2 AC3 6 HOH A1002 HOH A1248 SITE 1 AC4 12 SER A 184 GLU A 311 GLU A 324 ARG A 328 SITE 2 AC4 12 ADP A 501 MG A 502 MG A 503 HOH A1001 SITE 3 AC4 12 HOH A1002 HOH A1266 HOH A1267 HOH A1383 CRYST1 90.581 90.581 252.654 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 0.011040 0.006374 0.000000 0.00000 SCALE2 0.000000 0.012748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003958 0.00000