HEADER HYDROLASE 11-SEP-09 2WT4 TITLE ROOM TEMPERATURE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI L- TITLE 2 ASPARAGINASE AT 1.8 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-ASPARAGINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-ASNASE; COMPND 5 EC: 3.5.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.DHAVALA,A.C.PAPAGEORGIOU REVDAT 4 24-JUL-19 2WT4 1 REMARK REVDAT 3 30-MAY-12 2WT4 1 JRNL REMARK REVDAT 2 13-JUL-11 2WT4 1 VERSN REVDAT 1 24-NOV-09 2WT4 0 JRNL AUTH P.DHAVALA,A.C.PAPAGEORGIOU JRNL TITL STRUCTURE OF HELICOBACTER PYLORI L-ASPARAGINASE AT 1.4 A JRNL TITL 2 RESOLUTION JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 1253 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19966411 JRNL DOI 10.1107/S0907444909038244 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28339 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1474 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2048 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.1970 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2373 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.10000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.303 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2480 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3373 ; 1.321 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 5.455 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;41.540 ;25.446 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 443 ;12.528 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;16.619 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 403 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1837 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 991 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1756 ; 0.295 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 122 ; 0.122 ; 0.200 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): 57 ; 0.284 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.261 ; 0.200 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): 1637 ; 0.846 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2574 ; 1.343 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 934 ; 2.247 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 788 ; 3.451 ; 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 : 5 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 5 A 84 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1490 -15.6800 -21.5400 REMARK 3 T TENSOR REMARK 3 T11: 0.0783 T22: 0.1379 REMARK 3 T33: 0.0448 T12: 0.0097 REMARK 3 T13: 0.0421 T23: -0.0393 REMARK 3 L TENSOR REMARK 3 L11: 1.0251 L22: 1.2871 REMARK 3 L33: 1.3190 L12: -0.3185 REMARK 3 L13: -0.2708 L23: 0.3967 REMARK 3 S TENSOR REMARK 3 S11: -0.0206 S12: 0.1877 S13: -0.1525 REMARK 3 S21: -0.2721 S22: 0.0489 S23: -0.1896 REMARK 3 S31: 0.1224 S32: 0.1699 S33: -0.0283 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 85 A 146 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6050 -8.5500 -16.8090 REMARK 3 T TENSOR REMARK 3 T11: 0.0624 T22: 0.0876 REMARK 3 T33: 0.0702 T12: 0.0067 REMARK 3 T13: 0.0223 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 0.0469 L22: 0.5082 REMARK 3 L33: 1.1334 L12: 0.0699 REMARK 3 L13: -0.2241 L23: -0.1738 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: 0.0529 S13: -0.0248 REMARK 3 S21: -0.1144 S22: 0.0131 S23: -0.1147 REMARK 3 S31: -0.0365 S32: 0.1098 S33: -0.0247 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 147 A 209 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0100 -4.5230 -7.6310 REMARK 3 T TENSOR REMARK 3 T11: 0.0622 T22: 0.0855 REMARK 3 T33: 0.0812 T12: 0.0070 REMARK 3 T13: 0.0069 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.2312 L22: 0.4144 REMARK 3 L33: 0.7673 L12: -0.0748 REMARK 3 L13: 0.2088 L23: -0.0712 REMARK 3 S TENSOR REMARK 3 S11: 0.0217 S12: 0.0336 S13: 0.0177 REMARK 3 S21: -0.0165 S22: 0.0051 S23: -0.0627 REMARK 3 S31: -0.0508 S32: 0.0884 S33: -0.0267 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 210 A 317 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1890 -25.9490 5.7700 REMARK 3 T TENSOR REMARK 3 T11: 0.0730 T22: 0.0228 REMARK 3 T33: 0.0494 T12: 0.0304 REMARK 3 T13: -0.0109 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 1.3288 L22: 1.1432 REMARK 3 L33: 1.3084 L12: -0.0231 REMARK 3 L13: 0.0592 L23: -0.3165 REMARK 3 S TENSOR REMARK 3 S11: -0.0053 S12: -0.0432 S13: -0.1311 REMARK 3 S21: 0.0260 S22: 0.0030 S23: -0.0739 REMARK 3 S31: 0.1966 S32: 0.0765 S33: 0.0024 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 318 A 332 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0070 -21.7960 6.6600 REMARK 3 T TENSOR REMARK 3 T11: 0.0475 T22: 0.1363 REMARK 3 T33: 0.0964 T12: 0.0746 REMARK 3 T13: -0.0408 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 3.8939 L22: 11.7092 REMARK 3 L33: 8.3478 L12: -1.1498 REMARK 3 L13: -0.5093 L23: -3.5756 REMARK 3 S TENSOR REMARK 3 S11: -0.0371 S12: -0.2299 S13: -0.2905 REMARK 3 S21: 0.0395 S22: -0.1534 S23: -0.5756 REMARK 3 S31: 0.4825 S32: 0.5306 S33: 0.1905 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY REMARK 4 REMARK 4 2WT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1290041106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : BENT VERTICAL FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29828 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17.5% (W/V) PEG 4000, 0.1 M MG REMARK 280 FORMATE, 0.1 M HEPES-NAOH, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.45450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.18450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 50.93400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.45450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.18450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.93400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.45450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.18450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.93400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.45450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.18450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.93400 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 ASN A 4 REMARK 465 VAL A 22 REMARK 465 ASP A 23 REMARK 465 ALA A 24 REMARK 465 SER A 25 REMARK 465 LEU A 26 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 TYR A 29 REMARK 465 LYS A 30 REMARK 465 SER A 31 REMARK 465 GLY A 32 REMARK 465 GLU A 33 REMARK 465 LEU A 34 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 LYS A 37 CG CD CE NZ 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 CG MET A 197 O HOH A 2089 4555 2.09 REMARK 500 O HOH A 2043 O HOH A 2063 2555 2.12 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 GLU A 137 CB GLU A 137 CG -0.203 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 LYS A 37 112.91 -162.89 REMARK 500 GLU A 38 96.37 43.31 REMARK 500 LEU A 39 150.54 76.40 REMARK 500 LEU A 40 -54.18 66.34 REMARK 500 SER A 182 -104.38 -122.87 REMARK 500 SER A 182 -105.12 -122.26 REMARK 500 THR A 204 -108.82 39.60 REMARK 500 PRO A 232 25.42 -78.98 REMARK 500 SER A 277 -161.50 -111.02 REMARK 500 ASP A 301 -138.15 50.63 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 ASP A 3613 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WLT RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI L-ASPARAGINASE AT REMARK 900 ATOMIC RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE THREE CONFLICT INDICATED ARISE AS A RESULT OF REMARK 999 THESE RESIDUES PLACED ACCORDING TO THE NATURE OF REMARK 999 ELECTRON DENSITY AT THIS POINT. DBREF 2WT4 A 1 332 UNP Q9ZLB9 ASPG_HELPJ 1 332 SEQADV 2WT4 GLU A 137 UNP Q9ZLB9 TYR 137 CONFLICT SEQADV 2WT4 SER A 162 UNP Q9ZLB9 ARG 162 CONFLICT SEQADV 2WT4 VAL A 174 UNP Q9ZLB9 ILE 174 CONFLICT SEQRES 1 A 332 MET ALA GLN ASN LEU PRO THR ILE ALA LEU LEU ALA THR SEQRES 2 A 332 GLY GLY THR ILE ALA GLY SER GLY VAL ASP ALA SER LEU SEQRES 3 A 332 GLY SER TYR LYS SER GLY GLU LEU GLY VAL LYS GLU LEU SEQRES 4 A 332 LEU LYS ALA ILE PRO SER LEU ASN LYS ILE ALA ARG ILE SEQRES 5 A 332 GLN GLY GLU GLN VAL SER ASN ILE GLY SER GLN ASP MET SEQRES 6 A 332 ASN GLU GLU ILE TRP PHE LYS LEU ALA GLN ARG ALA GLN SEQRES 7 A 332 GLU LEU LEU ASP ASP SER ARG ILE GLN GLY VAL VAL ILE SEQRES 8 A 332 THR HIS GLY THR ASP THR LEU GLU GLU SER ALA TYR PHE SEQRES 9 A 332 LEU ASN LEU VAL LEU HIS SER THR LYS PRO VAL VAL LEU SEQRES 10 A 332 VAL GLY ALA MET ARG ASN ALA SER SER LEU SER ALA ASP SEQRES 11 A 332 GLY ALA LEU ASN LEU TYR GLU ALA VAL SER VAL ALA VAL SEQRES 12 A 332 ASN GLU LYS SER ALA ASN LYS GLY VAL LEU VAL VAL MET SEQRES 13 A 332 ASP ASP THR ILE PHE SER VAL ARG GLU VAL VAL LYS THR SEQRES 14 A 332 HIS THR THR HIS VAL SER THR PHE LYS ALA LEU ASN SER SEQRES 15 A 332 GLY ALA ILE GLY SER VAL TYR TYR GLY LYS THR ARG TYR SEQRES 16 A 332 TYR MET GLN PRO LEU ARG LYS HIS THR THR GLU SER GLU SEQRES 17 A 332 PHE SER LEU SER GLN LEU LYS THR PRO LEU PRO LYS VAL SEQRES 18 A 332 ASP ILE ILE TYR THR HIS ALA GLY MET THR PRO ASP LEU SEQRES 19 A 332 PHE GLN ALA SER LEU ASN SER HIS ALA LYS GLY VAL VAL SEQRES 20 A 332 ILE ALA GLY VAL GLY ASN GLY ASN VAL SER ALA GLY PHE SEQRES 21 A 332 LEU LYS ALA MET GLN GLU ALA SER GLN MET GLY VAL VAL SEQRES 22 A 332 ILE VAL ARG SER SER ARG VAL GLY SER GLY GLY VAL THR SEQRES 23 A 332 SER GLY GLU ILE ASP ASP LYS ALA TYR GLY PHE ILE THR SEQRES 24 A 332 SER ASP ASN LEU ASN PRO GLN LYS ALA ARG VAL LEU LEU SEQRES 25 A 332 GLN LEU ALA LEU THR LYS THR ASN ASP LYS ALA LYS ILE SEQRES 26 A 332 GLN GLU MET PHE GLU GLU TYR HET ASP A3613 9 HETNAM ASP ASPARTIC ACID FORMUL 2 ASP C4 H7 N O4 FORMUL 3 HOH *168(H2 O) HELIX 1 1 ILE A 43 ILE A 49 5 7 HELIX 2 2 ASN A 66 ASP A 82 1 17 HELIX 3 3 THR A 97 LEU A 109 1 13 HELIX 4 4 ALA A 132 ASN A 144 1 13 HELIX 5 5 GLU A 145 ALA A 148 5 4 HELIX 6 6 HIS A 203 SER A 207 5 5 HELIX 7 7 SER A 210 LEU A 214 5 5 HELIX 8 8 PRO A 232 SER A 241 1 10 HELIX 9 9 PHE A 260 MET A 270 1 11 HELIX 10 10 ASN A 304 THR A 317 1 14 HELIX 11 11 ASP A 321 TYR A 332 1 12 SHEET 1 AA 6 ARG A 51 GLN A 56 0 SHEET 2 AA 6 THR A 7 ALA A 12 1 O ILE A 8 N GLN A 53 SHEET 3 AA 6 VAL A 90 THR A 92 1 O VAL A 90 N LEU A 11 SHEET 4 AA 6 VAL A 116 VAL A 118 1 O VAL A 116 N ILE A 91 SHEET 5 AA 6 LEU A 153 MET A 156 1 O LEU A 153 N LEU A 117 SHEET 6 AA 6 THR A 159 SER A 162 -1 O THR A 159 N MET A 156 SHEET 1 AB 2 VAL A 167 LYS A 168 0 SHEET 2 AB 2 PHE A 177 LYS A 178 -1 O LYS A 178 N VAL A 167 SHEET 1 AC 4 ILE A 223 TYR A 225 0 SHEET 2 AC 4 VAL A 247 ALA A 249 1 O VAL A 247 N ILE A 224 SHEET 3 AC 4 VAL A 275 ARG A 276 1 O VAL A 275 N ILE A 248 SHEET 4 AC 4 ILE A 298 THR A 299 1 O ILE A 298 N ARG A 276 CISPEP 1 VAL A 36 LYS A 37 0 1.24 CISPEP 2 LYS A 37 GLU A 38 0 0.70 CISPEP 3 THR A 216 PRO A 217 0 0.94 SITE 1 AC1 13 GLY A 15 THR A 16 GLY A 61 SER A 62 SITE 2 AC1 13 GLN A 63 GLY A 94 THR A 95 ASP A 96 SITE 3 AC1 13 ALA A 120 ASN A 255 GLU A 289 HOH A2040 SITE 4 AC1 13 HOH A2041 CRYST1 64.909 96.369 101.868 90.00 90.00 90.00 I 2 2 2 8 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 0.015406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009817 0.00000