HEADER LIGASE 19-DEC-13 3WO1 TITLE CRYSTAL STRUCTURE OF TRP332ALA MUTANT YWFE, AN L-AMINO ACID LIGASE, TITLE 2 WITH BOUND ADP-MG-ALA 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; COMPND 8 MUTATION: 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 3WO1 1 REMARK SEQADV LINK REVDAT 1 14-MAY-14 3WO1 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 27089 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1475 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1967 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3623 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.41000 REMARK 3 B22 (A**2) : -2.41000 REMARK 3 B33 (A**2) : 7.81000 REMARK 3 B12 (A**2) : -2.41000 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): 0.291 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.582 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3732 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3533 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5063 ; 1.344 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8175 ; 0.692 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 465 ; 7.862 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;40.446 ;25.621 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;17.302 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.345 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 567 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4220 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 796 ; 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 3 A 125 REMARK 3 ORIGIN FOR THE GROUP (A): 9.3149 5.6006 43.6409 REMARK 3 T TENSOR REMARK 3 T11: 0.3303 T22: 0.3669 REMARK 3 T33: 0.1413 T12: -0.0965 REMARK 3 T13: 0.1205 T23: 0.1246 REMARK 3 L TENSOR REMARK 3 L11: 1.6994 L22: 1.7820 REMARK 3 L33: 0.8816 L12: -0.0214 REMARK 3 L13: -0.2651 L23: -0.4708 REMARK 3 S TENSOR REMARK 3 S11: 0.1679 S12: -0.2036 S13: 0.1059 REMARK 3 S21: 0.1433 S22: -0.2325 S23: -0.1725 REMARK 3 S31: 0.0408 S32: -0.0489 S33: 0.0646 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): 32.3175 11.8260 41.3464 REMARK 3 T TENSOR REMARK 3 T11: 0.2315 T22: 0.3319 REMARK 3 T33: 0.3801 T12: -0.0103 REMARK 3 T13: 0.0830 T23: 0.3265 REMARK 3 L TENSOR REMARK 3 L11: 2.8427 L22: 6.8571 REMARK 3 L33: 3.5570 L12: 3.4880 REMARK 3 L13: 0.7385 L23: 0.1554 REMARK 3 S TENSOR REMARK 3 S11: 0.2537 S12: -0.2914 S13: -0.3142 REMARK 3 S21: 0.3389 S22: -0.5219 S23: -0.3941 REMARK 3 S31: -0.0510 S32: 0.2320 S33: 0.2682 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): 31.7498 25.6346 50.4964 REMARK 3 T TENSOR REMARK 3 T11: 0.6298 T22: 0.5529 REMARK 3 T33: 0.4332 T12: -0.3551 REMARK 3 T13: -0.0220 T23: 0.2732 REMARK 3 L TENSOR REMARK 3 L11: 3.1182 L22: 1.1892 REMARK 3 L33: 0.1612 L12: 0.3487 REMARK 3 L13: 0.3030 L23: 0.1162 REMARK 3 S TENSOR REMARK 3 S11: 0.4535 S12: -0.7658 S13: -0.0915 REMARK 3 S21: 0.6017 S22: -0.3971 S23: -0.3907 REMARK 3 S31: -0.0400 S32: -0.0122 S33: -0.0564 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): 15.9131 27.9178 34.0529 REMARK 3 T TENSOR REMARK 3 T11: 0.2437 T22: 0.2477 REMARK 3 T33: 0.4078 T12: 0.0113 REMARK 3 T13: 0.1885 T23: 0.2051 REMARK 3 L TENSOR REMARK 3 L11: 1.8709 L22: 1.4555 REMARK 3 L33: 0.6301 L12: 1.3003 REMARK 3 L13: -0.4098 L23: -0.4306 REMARK 3 S TENSOR REMARK 3 S11: 0.2453 S12: 0.0463 S13: 0.6042 REMARK 3 S21: 0.0168 S22: -0.1874 S23: 0.1305 REMARK 3 S31: -0.0583 S32: -0.0092 S33: -0.0578 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 3WO1 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_1000096576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28700 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 55.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.600 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 (%): 58.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.3M NACL, 0.1M HEPES REMARK 280 -NAOH, 5% ETHYLENE GLYCOL, 1MM DTT, PH 7.25, 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 172.50467 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 86.25233 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 129.37850 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 43.12617 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 215.63083 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 172.50467 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 86.25233 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 43.12617 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 129.37850 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 215.63083 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: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 86.25233 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 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 N SER A 185 O1B ADP A 501 2.05 REMARK 500 O PRO A 267 O HOH A 1045 2.08 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 OE1 GLN A 449 OE1 GLN A 449 10665 2.05 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 -160.55 -166.14 REMARK 500 ASN A 82 33.05 -91.72 REMARK 500 TYR A 181 -9.17 -142.57 REMARK 500 PRO A 214 170.45 -52.73 REMARK 500 TYR A 242 -152.95 -100.89 REMARK 500 ASP A 244 34.95 -96.03 REMARK 500 GLN A 304 -62.60 -102.66 REMARK 500 CYS A 306 163.65 179.70 REMARK 500 ALA A 327 42.56 -88.87 REMARK 500 ALA A 332 -145.91 55.61 REMARK 500 TYR A 372 170.52 171.93 REMARK 500 LEU A 429 43.65 -107.72 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 OE2 115.4 REMARK 620 3 ADP A 501 O1A 97.2 72.6 REMARK 620 4 ADP A 501 O3B 129.8 111.1 79.2 REMARK 620 5 HOH A1084 O 64.0 157.0 130.1 80.3 REMARK 620 N 1 2 3 4 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 ADP A 501 O2B REMARK 620 2 ADP A 501 O3B 57.3 REMARK 620 3 HOH A1021 O 132.4 75.5 REMARK 620 4 HOH A1086 O 108.8 139.3 110.8 REMARK 620 N 1 2 3 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 ALA A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VMM RELATED DB: PDB REMARK 900 THE SAME WILD-TYPE PROTEIN COMPLEXED WITH PHOSPHINOPHOSPHATE ANALOG REMARK 900 RELATED ID: 3WNZ RELATED DB: PDB REMARK 900 RELATED ID: 3WO0 RELATED DB: PDB DBREF 3WO1 A 4 468 UNP P39641 BACD_BACSU 4 468 SEQADV 3WO1 GLY A -1 UNP P39641 EXPRESSION TAG SEQADV 3WO1 PRO A 0 UNP P39641 EXPRESSION TAG SEQADV 3WO1 LEU A 1 UNP P39641 EXPRESSION TAG SEQADV 3WO1 GLY A 2 UNP P39641 EXPRESSION TAG SEQADV 3WO1 SER A 3 UNP P39641 EXPRESSION TAG SEQADV 3WO1 ALA A 332 UNP P39641 TRP 332 ENGINEERED MUTATION 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 ALA 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 ALA A 504 6 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ALA ALANINE FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG 2(MG 2+) FORMUL 5 ALA C3 H7 N O2 FORMUL 6 HOH *87(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 PHE A 99 1 16 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 ASP A 137 1 10 HELIX 10 10 ASP A 137 GLY A 149 1 13 HELIX 11 11 LEU A 161 GLY A 172 1 12 HELIX 12 12 ALA A 197 ASN A 205 1 9 HELIX 13 13 ASP A 206 SER A 210 5 5 HELIX 14 14 GLU A 232 TRP A 236 5 5 HELIX 15 15 ASP A 283 GLY A 302 1 20 HELIX 16 16 LYS A 316 ARG A 318 5 3 HELIX 17 17 ASN A 333 GLY A 343 1 11 HELIX 18 18 ASP A 345 GLY A 357 1 13 HELIX 19 19 LYS A 358 ALA A 360 5 3 HELIX 20 20 TYR A 380 GLN A 386 1 7 HELIX 21 21 PHE A 432 ASN A 436 5 5 HELIX 22 22 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 SER A 32 O ALA A 54 SHEET 3 A 4 THR A 5 ILE A 9 1 N VAL A 8 O VAL A 31 SHEET 4 A 4 ALA A 103 THR A 106 1 O ALA A 103 N LEU A 7 SHEET 1 B 3 ASN A 155 VAL A 158 0 SHEET 2 B 3 PHE A 223 GLU A 227 -1 O PHE A 223 N VAL A 158 SHEET 3 B 3 LEU A 175 PRO A 179 -1 N LYS A 178 O ILE A 224 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 HIS A 263 N SER A 247 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 ASP A 376 N HIS A 276 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 VAL A 416 O GLU A 442 SHEET 1 D 3 THR A 425 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 ALA A 466 -1 O LYS A 463 N ASP A 403 LINK OE1 GLU A 311 MG MG A 502 1555 1555 2.48 LINK OE2 GLU A 324 MG MG A 502 1555 1555 2.60 LINK O1A ADP A 501 MG MG A 502 1555 1555 1.98 LINK O3B ADP A 501 MG MG A 502 1555 1555 2.27 LINK O2B ADP A 501 MG MG A 503 1555 1555 2.49 LINK O3B ADP A 501 MG MG A 503 1555 1555 2.83 LINK MG MG A 502 O HOH A1084 1555 1555 2.48 LINK MG MG A 503 O HOH A1021 1555 1555 2.37 LINK MG MG A 503 O HOH A1086 1555 1555 2.18 CISPEP 1 THR A 173 PRO A 174 0 -7.08 CISPEP 2 THR A 278 PRO A 279 0 -11.99 SITE 1 AC1 17 LYS A 138 LYS A 178 LEU A 182 ALA A 183 SITE 2 AC1 17 SER A 184 SER A 185 GLU A 226 GLU A 227 SITE 3 AC1 17 PHE A 228 LEU A 229 GLN A 268 GLU A 311 SITE 4 AC1 17 GLU A 324 MG A 502 MG A 503 HOH A1084 SITE 5 AC1 17 HOH A1087 SITE 1 AC2 6 GLU A 311 GLU A 324 ADP A 501 MG A 503 SITE 2 AC2 6 HOH A1021 HOH A1084 SITE 1 AC3 5 GLU A 324 ADP A 501 MG A 502 HOH A1021 SITE 2 AC3 5 HOH A1086 SITE 1 AC4 9 GLU A 273 HIS A 309 GLU A 311 ARG A 328 SITE 2 AC4 9 ALA A 330 GLY A 331 MET A 334 HOH A1021 SITE 3 AC4 9 HOH A1084 CRYST1 91.129 91.129 258.757 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 0.010973 0.006336 0.000000 0.00000 SCALE2 0.000000 0.012671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003865 0.00000