HEADER IMMUNE SYSTEM 13-MAR-09 2WCR TITLE CRYSTAL STRUCTURE OF TIP-ALPHA N34 (HP0596) FROM HELICOBACTER PYLORI TITLE 2 AT PH8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNF-ALPHA INDUCER PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FRAGMENT AFTER TRYPSIN DIGESTION, RESIDUES 34-192; COMPND 5 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: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET151-D TOPO KEYWDS HP0596, TIP-ALPHA, HELICOBACTER PYLORI, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.TOSI,G.CIOCI,K.JOURAVLEVA,C.DIAN,L.TERRADOT REVDAT 4 13-DEC-23 2WCR 1 REMARK LINK REVDAT 3 13-JUL-11 2WCR 1 VERSN REVDAT 2 26-MAY-09 2WCR 1 JRNL REVDAT 1 12-MAY-09 2WCR 0 JRNL AUTH T.TOSI,G.CIOCI,K.JOURAVLEVA,C.DIAN,L.TERRADOT JRNL TITL STRUCTURES OF THE TUMOR NECROSIS FACTOR ALPHA INDUCING JRNL TITL 2 PROTEIN TIPALPHA: A NOVEL VIRULENCE FACTOR FROM HELICOBACTER JRNL TITL 3 PYLORI. JRNL REF FEBS LETT. V. 583 1581 2009 JRNL REFN ISSN 0014-5793 JRNL PMID 19401200 JRNL DOI 10.1016/J.FEBSLET.2009.04.033 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 34065 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1788 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2478 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 130 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2354 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 26.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.11000 REMARK 3 B22 (A**2) : -0.87000 REMARK 3 B33 (A**2) : -0.24000 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): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.180 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2529 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1742 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3437 ; 1.520 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4293 ; 0.995 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.640 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;31.589 ;24.960 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 505 ;14.335 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;18.738 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2809 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 492 ; 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): 1521 ; 0.895 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 608 ; 0.283 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2498 ; 1.574 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1008 ; 2.744 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 919 ; 4.513 ; 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 : 6 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 34 A 51 REMARK 3 ORIGIN FOR THE GROUP (A): 34.6424 42.0244 6.0959 REMARK 3 T TENSOR REMARK 3 T11: 0.1234 T22: 0.0926 REMARK 3 T33: 0.1102 T12: -0.0049 REMARK 3 T13: 0.0050 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.3788 L22: 3.4843 REMARK 3 L33: 4.3267 L12: 1.9004 REMARK 3 L13: -0.3494 L23: -0.7886 REMARK 3 S TENSOR REMARK 3 S11: 0.1889 S12: -0.1561 S13: 0.2133 REMARK 3 S21: 0.1371 S22: 0.0153 S23: 0.3876 REMARK 3 S31: -0.5649 S32: -0.2832 S33: -0.2042 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 52 A 144 REMARK 3 ORIGIN FOR THE GROUP (A): 30.9496 33.2292 21.5705 REMARK 3 T TENSOR REMARK 3 T11: 0.0481 T22: 0.0860 REMARK 3 T33: 0.1391 T12: 0.0107 REMARK 3 T13: -0.0124 T23: 0.0194 REMARK 3 L TENSOR REMARK 3 L11: 0.5468 L22: 0.8180 REMARK 3 L33: 2.2904 L12: -0.2585 REMARK 3 L13: -0.5051 L23: 0.1278 REMARK 3 S TENSOR REMARK 3 S11: 0.0629 S12: 0.0801 S13: -0.0593 REMARK 3 S21: 0.0267 S22: 0.0282 S23: 0.1686 REMARK 3 S31: -0.0309 S32: -0.2069 S33: -0.0911 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 145 A 180 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6337 36.1466 33.9652 REMARK 3 T TENSOR REMARK 3 T11: 0.0711 T22: 0.1229 REMARK 3 T33: 0.1788 T12: 0.0829 REMARK 3 T13: 0.0866 T23: 0.0862 REMARK 3 L TENSOR REMARK 3 L11: 2.0838 L22: 2.7683 REMARK 3 L33: 5.1499 L12: 0.5493 REMARK 3 L13: -0.2830 L23: 0.1007 REMARK 3 S TENSOR REMARK 3 S11: 0.1475 S12: 0.2234 S13: 0.0240 REMARK 3 S21: 0.0365 S22: 0.0952 S23: 0.3230 REMARK 3 S31: -0.3841 S32: -0.6231 S33: -0.2427 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 : B 35 B 51 REMARK 3 ORIGIN FOR THE GROUP (A): 39.7201 41.9200 7.0997 REMARK 3 T TENSOR REMARK 3 T11: 0.1197 T22: 0.1545 REMARK 3 T33: 0.2345 T12: 0.0414 REMARK 3 T13: -0.0975 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 2.5902 L22: 1.7018 REMARK 3 L33: 9.7497 L12: 1.2081 REMARK 3 L13: 4.2097 L23: 1.8131 REMARK 3 S TENSOR REMARK 3 S11: 0.3995 S12: -0.1827 S13: -0.4500 REMARK 3 S21: 0.1323 S22: 0.0225 S23: 0.0336 REMARK 3 S31: 0.7517 S32: -0.0256 S33: -0.4220 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 : B 52 B 142 REMARK 3 ORIGIN FOR THE GROUP (A): 40.8146 53.8518 19.0169 REMARK 3 T TENSOR REMARK 3 T11: 0.0547 T22: 0.0654 REMARK 3 T33: 0.0802 T12: 0.0035 REMARK 3 T13: 0.0001 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.8315 L22: 1.0819 REMARK 3 L33: 2.1273 L12: -0.1955 REMARK 3 L13: 0.5427 L23: -0.2925 REMARK 3 S TENSOR REMARK 3 S11: 0.0688 S12: 0.1033 S13: -0.0564 REMARK 3 S21: 0.0051 S22: 0.0014 S23: 0.0352 REMARK 3 S31: -0.1653 S32: 0.0489 S33: -0.0702 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 143 B 180 REMARK 3 ORIGIN FOR THE GROUP (A): 50.4921 54.4959 31.5414 REMARK 3 T TENSOR REMARK 3 T11: 0.0781 T22: 0.0942 REMARK 3 T33: 0.0993 T12: -0.0227 REMARK 3 T13: -0.0372 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 2.0738 L22: 2.8243 REMARK 3 L33: 3.9123 L12: 0.6957 REMARK 3 L13: 0.5710 L23: -0.9638 REMARK 3 S TENSOR REMARK 3 S11: 0.1092 S12: 0.0712 S13: -0.0582 REMARK 3 S21: 0.2441 S22: -0.0448 S23: -0.0356 REMARK 3 S31: -0.0528 S32: 0.1390 S33: -0.0644 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. U VALUES RESIDUAL ONLY REMARK 4 REMARK 4 2WCR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290038532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.981 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35854 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 27.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.570 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2WCQ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 8.5, 26% PEG4000, 50 MM REMARK 280 MGCL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.73500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.73500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.63000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 182 REMARK 465 TYR A 183 REMARK 465 GLY A 184 REMARK 465 ASP A 185 REMARK 465 VAL A 186 REMARK 465 LYS A 187 REMARK 465 VAL A 188 REMARK 465 PRO A 189 REMARK 465 ILE A 190 REMARK 465 ALA A 191 REMARK 465 MET A 192 REMARK 465 ASN B 34 REMARK 465 ASN B 182 REMARK 465 TYR B 183 REMARK 465 GLY B 184 REMARK 465 ASP B 185 REMARK 465 VAL B 186 REMARK 465 LYS B 187 REMARK 465 VAL B 188 REMARK 465 PRO B 189 REMARK 465 ILE B 190 REMARK 465 ALA B 191 REMARK 465 MET B 192 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 149 CG CD CE NZ REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 VAL A 181 CA C O CB CG1 CG2 REMARK 470 GLN B 46 OE1 NE2 REMARK 470 LYS B 66 CD CE NZ REMARK 470 LYS B 104 CD CE NZ REMARK 470 VAL B 181 CA C O CB CG1 CG2 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 OE2 GLU A 154 O HOH A 2163 1.91 REMARK 500 ND2 ASN B 135 O HOH B 2131 1.95 REMARK 500 OD1 ASP A 63 O HOH A 2040 2.14 REMARK 500 NE2 HIS B 88 O HOH B 2069 2.16 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 SER A 49 121.33 159.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 48 SER A 49 -148.88 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 NI A 400 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 34 N REMARK 620 2 ASN A 34 OD1 87.3 REMARK 620 3 ASN A 34 O 81.8 88.0 REMARK 620 4 HIS A 157 NE2 96.5 173.3 87.0 REMARK 620 5 IMD A 300 N3 164.9 79.5 90.5 96.0 REMARK 620 6 HIS B 60 NE2 89.5 89.0 171.0 96.6 97.3 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 IMD A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WCQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TIP-ALPHA N34 (HP0596) FROM HELICOBACTER REMARK 900 PYLORI AT PH4 DBREF 2WCR A 34 192 UNP O25318 O25318_HELPY 34 192 DBREF 2WCR B 34 192 UNP O25318 O25318_HELPY 34 192 SEQRES 1 A 159 ASN SER PHE LEU GLN ASP VAL PRO TYR TRP MET LEU GLN SEQRES 2 A 159 ASN ARG SER GLU TYR ILE THR GLN GLY VAL ASP SER SER SEQRES 3 A 159 HIS ILE VAL ASP GLY LYS LYS THR GLU GLU ILE GLU LYS SEQRES 4 A 159 ILE ALA THR LYS ARG ALA THR ILE ARG VAL ALA GLN ASN SEQRES 5 A 159 ILE VAL HIS LYS LEU LYS GLU ALA TYR LEU SER LYS THR SEQRES 6 A 159 ASN ARG ILE LYS GLN LYS ILE THR ASN GLU MET PHE ILE SEQRES 7 A 159 GLN MET THR GLN PRO ILE TYR ASP SER LEU MET ASN VAL SEQRES 8 A 159 ASP ARG LEU GLY ILE TYR ILE ASN PRO ASN ASN GLU GLU SEQRES 9 A 159 VAL PHE ALA LEU VAL ARG ALA ARG GLY PHE ASP LYS ASP SEQRES 10 A 159 ALA LEU SER GLU GLY LEU HIS LYS MET SER LEU ASP ASN SEQRES 11 A 159 GLN ALA VAL SER ILE LEU VAL ALA LYS VAL GLU GLU ILE SEQRES 12 A 159 PHE LYS ASP SER VAL ASN TYR GLY ASP VAL LYS VAL PRO SEQRES 13 A 159 ILE ALA MET SEQRES 1 B 159 ASN SER PHE LEU GLN ASP VAL PRO TYR TRP MET LEU GLN SEQRES 2 B 159 ASN ARG SER GLU TYR ILE THR GLN GLY VAL ASP SER SER SEQRES 3 B 159 HIS ILE VAL ASP GLY LYS LYS THR GLU GLU ILE GLU LYS SEQRES 4 B 159 ILE ALA THR LYS ARG ALA THR ILE ARG VAL ALA GLN ASN SEQRES 5 B 159 ILE VAL HIS LYS LEU LYS GLU ALA TYR LEU SER LYS THR SEQRES 6 B 159 ASN ARG ILE LYS GLN LYS ILE THR ASN GLU MET PHE ILE SEQRES 7 B 159 GLN MET THR GLN PRO ILE TYR ASP SER LEU MET ASN VAL SEQRES 8 B 159 ASP ARG LEU GLY ILE TYR ILE ASN PRO ASN ASN GLU GLU SEQRES 9 B 159 VAL PHE ALA LEU VAL ARG ALA ARG GLY PHE ASP LYS ASP SEQRES 10 B 159 ALA LEU SER GLU GLY LEU HIS LYS MET SER LEU ASP ASN SEQRES 11 B 159 GLN ALA VAL SER ILE LEU VAL ALA LYS VAL GLU GLU ILE SEQRES 12 B 159 PHE LYS ASP SER VAL ASN TYR GLY ASP VAL LYS VAL PRO SEQRES 13 B 159 ILE ALA MET HET IMD A 300 5 HET NI A 400 1 HETNAM IMD IMIDAZOLE HETNAM NI NICKEL (II) ION FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 NI NI 2+ FORMUL 5 HOH *354(H2 O) HELIX 1 1 PRO A 41 MET A 44 5 4 HELIX 2 2 LYS A 66 SER A 96 1 31 HELIX 3 3 THR A 106 SER A 120 1 15 HELIX 4 4 ASP A 148 LYS A 158 1 11 HELIX 5 5 ASP A 162 SER A 180 1 19 HELIX 6 6 LYS B 66 SER B 96 1 31 HELIX 7 7 THR B 106 MET B 113 1 8 HELIX 8 8 MET B 113 SER B 120 1 8 HELIX 9 9 ASP B 148 MET B 159 1 12 HELIX 10 10 ASP B 162 SER B 180 1 19 SHEET 1 AA 2 PHE A 36 LEU A 37 0 SHEET 2 AA 2 VAL B 40 PRO B 41 -1 O VAL B 40 N LEU A 37 SHEET 1 AB 3 GLN A 54 SER A 59 0 SHEET 2 AB 3 VAL A 138 PHE A 147 -1 O VAL A 138 N SER A 59 SHEET 3 AB 3 LEU A 121 ILE A 131 -1 O MET A 122 N GLY A 146 SHEET 1 BA 3 GLN B 54 HIS B 60 0 SHEET 2 BA 3 GLU B 137 PHE B 147 -1 O VAL B 138 N SER B 59 SHEET 3 BA 3 LEU B 121 ASN B 132 -1 O MET B 122 N GLY B 146 LINK N ASN A 34 NI NI A 400 2665 1555 1.96 LINK OD1 ASN A 34 NI NI A 400 2665 1555 2.09 LINK O ASN A 34 NI NI A 400 2665 1555 2.17 LINK NE2 HIS A 157 NI NI A 400 1555 1555 2.02 LINK N3 IMD A 300 NI NI A 400 1555 1555 2.20 LINK NI NI A 400 NE2 HIS B 60 1555 3645 2.09 SITE 1 AC1 7 ASN A 34 PHE A 36 HIS A 157 LYS A 158 SITE 2 AC1 7 NI A 400 HOH A2169 HIS B 60 SITE 1 AC2 4 ASN A 34 HIS A 157 IMD A 300 HIS B 60 CRYST1 48.880 67.260 97.470 90.00 90.00 90.00 P 21 21 21 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 0.020458 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010260 0.00000