PDB Short entry for 1E9Z HEADER HYDROLASE 01-NOV-00 1E9Z TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREASE SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UREA AMIDOHYDROLASE SUBUNIT ALPHA; COMPND 5 EC: 3.5.1.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UREASE SUBUNIT BETA; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: UREA AMIDOHYDROLASE SUBUNIT BETA; COMPND 11 EC: 3.5.1.5; COMPND 12 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; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 8 ORGANISM_TAXID: 210; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.-C.HA,S.-T.OH,B.-H.OH REVDAT 6 13-DEC-23 1E9Z 1 REMARK LINK REVDAT 5 04-APR-18 1E9Z 1 REMARK REVDAT 4 25-AUG-10 1E9Z 1 VERSN REVDAT 3 24-FEB-09 1E9Z 1 VERSN REVDAT 2 13-FEB-07 1E9Z 1 KEYWDS JRNL REVDAT 1 01-NOV-01 1E9Z 0 JRNL AUTH N.-C.HA,S.-T.OH,J.Y.SUNG,K.-A.CHA,M.HYUNG LEE,B.-H.OH JRNL TITL SUPRAMOLECULAR ASSEMBLY AND ACID RESISTANCE OF HELICOBACTER JRNL TITL 2 PYLORI UREASE JRNL REF NAT.STRUCT.BIOL. V. 8 480 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11373617 JRNL DOI 10.1038/88563 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 17148 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6198 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.260 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1E9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-NOV-00. REMARK 100 THE DEPOSITION ID IS D_1290005504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MACSCIENCE M18X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21702 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.11500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1KAU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 88.95500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 88.95500 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 88.95500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 88.95500 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 88.95500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 88.95500 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 88.95500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 88.95500 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 88.95500 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 88.95500 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 88.95500 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 88.95500 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 88.95500 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 88.95500 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 88.95500 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 88.95500 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 88.95500 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 88.95500 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 88.95500 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 88.95500 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 88.95500 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 88.95500 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 88.95500 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 88.95500 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 88.95500 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 88.95500 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: 24-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 24-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 206850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 236120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1311.8 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 177.91000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 177.91000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 0.000000 -1.000000 177.91000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 177.91000 REMARK 350 BIOMT3 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 177.91000 REMARK 350 BIOMT2 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 4 -1.000000 0.000000 0.000000 177.91000 REMARK 350 BIOMT1 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 6 0.000000 -1.000000 0.000000 177.91000 REMARK 350 BIOMT2 6 0.000000 0.000000 -1.000000 177.91000 REMARK 350 BIOMT3 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 0.000000 0.000000 -1.000000 177.91000 REMARK 350 BIOMT3 7 -1.000000 0.000000 0.000000 177.91000 REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 0.000000 -1.000000 0.000000 177.91000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 177.91000 REMARK 350 BIOMT1 9 0.000000 0.000000 -1.000000 177.91000 REMARK 350 BIOMT2 9 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 -1.000000 0.000000 177.91000 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 177.91000 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 177.91000 REMARK 350 BIOMT1 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 11 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 12 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 12 -1.000000 0.000000 0.000000 177.91000 REMARK 350 BIOMT3 12 0.000000 -1.000000 0.000000 177.91000 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 2 93.95 -31.83 REMARK 500 TYR A 32 -70.43 -41.11 REMARK 500 ALA A 37 -72.88 -49.32 REMARK 500 LYS A 51 -77.76 -95.60 REMARK 500 THR A 98 74.39 27.28 REMARK 500 ALA A 102 45.75 -57.55 REMARK 500 ASN A 115 152.80 -41.19 REMARK 500 GLU A 116 174.75 132.64 REMARK 500 GLU A 122 155.32 -36.92 REMARK 500 LYS A 125 103.75 7.88 REMARK 500 HIS A 144 38.48 -95.39 REMARK 500 HIS A 146 99.65 -56.61 REMARK 500 ASN A 151 138.07 -25.51 REMARK 500 ARG A 152 26.60 -69.20 REMARK 500 LEU A 154 95.12 -63.12 REMARK 500 PHE A 156 -179.88 -177.88 REMARK 500 LEU A 166 102.88 -44.67 REMARK 500 ASP A 167 84.06 -57.29 REMARK 500 THR A 172 -173.74 -55.22 REMARK 500 PHE A 198 -100.89 64.66 REMARK 500 VAL A 202 -72.70 -104.80 REMARK 500 ARG A 204 -152.51 -153.54 REMARK 500 ALA A 206 89.75 -61.68 REMARK 500 LYS A 227 -139.76 24.55 REMARK 500 ASN A 231 70.85 56.41 REMARK 500 LYS B 2 166.13 -44.67 REMARK 500 TYR B 9 -54.88 -28.55 REMARK 500 THR B 17 149.90 -39.35 REMARK 500 VAL B 32 106.46 -57.12 REMARK 500 TYR B 39 106.06 -23.32 REMARK 500 LYS B 49 -150.42 -55.89 REMARK 500 LEU B 51 81.30 -67.46 REMARK 500 GLU B 53 136.14 -34.33 REMARK 500 MET B 55 -105.92 -94.89 REMARK 500 LYS B 63 41.43 -72.75 REMARK 500 GLU B 64 -2.38 -142.13 REMARK 500 GLU B 65 115.99 -19.72 REMARK 500 ILE B 81 74.16 -108.77 REMARK 500 ALA B 84 169.19 165.79 REMARK 500 LYS B 98 -81.00 -79.10 REMARK 500 PHE B 139 70.48 -62.77 REMARK 500 THR B 161 28.84 -140.77 REMARK 500 PRO B 163 27.18 -50.85 REMARK 500 SER B 190 79.79 -111.37 REMARK 500 MET B 191 105.25 172.44 REMARK 500 ASN B 192 135.00 -35.62 REMARK 500 ASN B 200 78.06 -67.72 REMARK 500 ALA B 201 135.22 -172.32 REMARK 500 THR B 249 148.33 -27.25 REMARK 500 LEU B 252 -11.46 -45.14 REMARK 500 REMARK 500 THIS ENTRY HAS 99 RAMACHANDRAN OUTLIERS. 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 B3002 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 136 NE2 REMARK 620 2 HIS B 138 NE2 92.4 REMARK 620 3 KCX B 219 OQ2 78.6 104.3 REMARK 620 4 ASP B 362 OD1 65.8 86.3 143.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B3001 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX B 219 OQ2 REMARK 620 2 HIS B 248 ND1 86.0 REMARK 620 3 HIS B 274 NE2 110.9 64.0 REMARK 620 4 HOH B2027 O 137.8 111.9 111.3 REMARK 620 5 NI B3002 NI 66.1 151.9 128.1 88.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 3002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E9Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE IN COMPLEX WITH REMARK 900 ACETOHYDROXAMIC ACID DBREF 1E9Z A 1 238 UNP P14916 URE23_HELPY 1 238 DBREF 1E9Z B 1 569 UNP P69996 URE1_HELPY 1 569 SEQADV 1E9Z KCX B 219 UNP P14917 LYS 219 MODIFIED RESIDUE SEQADV 1E9Z ALA A 170 UNP P14916 SER 170 CONFLICT SEQADV 1E9Z ALA B 355 UNP P69996 ILE 355 CONFLICT SEQADV 1E9Z VAL B 522 UNP P69996 ILE 522 CONFLICT SEQADV 1E9Z ASN B 531 UNP P69996 ASP 531 CONFLICT SEQRES 1 A 238 MET LYS LEU THR PRO LYS GLU LEU ASP LYS LEU MET LEU SEQRES 2 A 238 HIS TYR ALA GLY GLU LEU ALA LYS LYS ARG LYS GLU LYS SEQRES 3 A 238 GLY ILE LYS LEU ASN TYR VAL GLU ALA VAL ALA LEU ILE SEQRES 4 A 238 SER ALA HIS ILE MET GLU GLU ALA ARG ALA GLY LYS LYS SEQRES 5 A 238 THR ALA ALA GLU LEU MET GLN GLU GLY ARG THR LEU LEU SEQRES 6 A 238 LYS PRO ASP ASP VAL MET ASP GLY VAL ALA SER MET ILE SEQRES 7 A 238 HIS GLU VAL GLY ILE GLU ALA MET PHE PRO ASP GLY THR SEQRES 8 A 238 LYS LEU VAL THR VAL HIS THR PRO ILE GLU ALA ASN GLY SEQRES 9 A 238 LYS LEU VAL PRO GLY GLU LEU PHE LEU LYS ASN GLU ASP SEQRES 10 A 238 ILE THR ILE ASN GLU GLY LYS LYS ALA VAL SER VAL LYS SEQRES 11 A 238 VAL LYS ASN VAL GLY ASP ARG PRO VAL GLN ILE GLY SER SEQRES 12 A 238 HIS PHE HIS PHE PHE GLU VAL ASN ARG CYS LEU ASP PHE SEQRES 13 A 238 ASP ARG GLU LYS THR PHE GLY LYS ARG LEU ASP ILE ALA SEQRES 14 A 238 ALA GLY THR ALA VAL ARG PHE GLU PRO GLY GLU GLU LYS SEQRES 15 A 238 SER VAL GLU LEU ILE ASP ILE GLY GLY ASN ARG ARG ILE SEQRES 16 A 238 PHE GLY PHE ASN ALA LEU VAL ASP ARG GLN ALA ASP ASN SEQRES 17 A 238 GLU SER LYS LYS ILE ALA LEU HIS ARG ALA LYS GLU ARG SEQRES 18 A 238 GLY PHE HIS GLY ALA LYS SER ASP ASP ASN TYR VAL LYS SEQRES 19 A 238 THR ILE LYS GLU SEQRES 1 B 569 MET LYS LYS ILE SER ARG LYS GLU TYR VAL SER MET TYR SEQRES 2 B 569 GLY PRO THR THR GLY ASP LYS VAL ARG LEU GLY ASP THR SEQRES 3 B 569 ASP LEU ILE ALA GLU VAL GLU HIS ASP TYR THR ILE TYR SEQRES 4 B 569 GLY GLU GLU LEU LYS PHE GLY GLY GLY LYS THR LEU ARG SEQRES 5 B 569 GLU GLY MET SER GLN SER ASN ASN PRO SER LYS GLU GLU SEQRES 6 B 569 LEU ASP LEU ILE ILE THR ASN ALA LEU ILE VAL ASP TYR SEQRES 7 B 569 THR GLY ILE TYR LYS ALA ASP ILE GLY ILE LYS ASP GLY SEQRES 8 B 569 LYS ILE ALA GLY ILE GLY LYS GLY GLY ASN LYS ASP MET SEQRES 9 B 569 GLN ASP GLY VAL LYS ASN ASN LEU SER VAL GLY PRO ALA SEQRES 10 B 569 THR GLU ALA LEU ALA GLY GLU GLY LEU ILE VAL THR ALA SEQRES 11 B 569 GLY GLY ILE ASP THR HIS ILE HIS PHE ILE SER PRO GLN SEQRES 12 B 569 GLN ILE PRO THR ALA PHE ALA SER GLY VAL THR THR MET SEQRES 13 B 569 ILE GLY GLY GLY THR GLY PRO ALA ASP GLY THR ASN ALA SEQRES 14 B 569 THR THR ILE THR PRO GLY ARG ARG ASN LEU LYS TRP MET SEQRES 15 B 569 LEU ARG ALA ALA GLU GLU TYR SER MET ASN LEU GLY PHE SEQRES 16 B 569 LEU ALA LYS GLY ASN ALA SER ASN ASP ALA SER LEU ALA SEQRES 17 B 569 ASP GLN ILE GLU ALA GLY ALA ILE GLY PHE KCX ILE HIS SEQRES 18 B 569 GLU ASP TRP GLY THR THR PRO SER ALA ILE ASN HIS ALA SEQRES 19 B 569 LEU ASP VAL ALA ASP LYS TYR ASP VAL GLN VAL ALA ILE SEQRES 20 B 569 HIS THR ASP THR LEU ASN GLU ALA GLY CYS VAL GLU ASP SEQRES 21 B 569 THR MET ALA ALA ILE ALA GLY ARG THR MET HIS THR PHE SEQRES 22 B 569 HIS THR GLU GLY ALA GLY GLY GLY HIS ALA PRO ASP ILE SEQRES 23 B 569 ILE LYS VAL ALA GLY GLU HIS ASN ILE LEU PRO ALA SER SEQRES 24 B 569 THR ASN PRO THR ILE PRO PHE THR VAL ASN THR GLU ALA SEQRES 25 B 569 GLU HIS MET ASP MET LEU MET VAL CYS HIS HIS LEU ASP SEQRES 26 B 569 LYS SER ILE LYS GLU ASP VAL GLN PHE ALA ASP SER ARG SEQRES 27 B 569 ILE ARG PRO GLN THR ILE ALA ALA GLU ASP THR LEU HIS SEQRES 28 B 569 ASP MET GLY ALA PHE SER ILE THR SER SER ASP SER GLN SEQRES 29 B 569 ALA MET GLY ARG VAL GLY GLU VAL ILE THR ARG THR TRP SEQRES 30 B 569 GLN THR ALA ASP LYS ASN LYS LYS GLU PHE GLY ARG LEU SEQRES 31 B 569 LYS GLU GLU LYS GLY ASP ASN ASP ASN PHE ARG ILE LYS SEQRES 32 B 569 ARG TYR LEU SER LYS TYR THR ILE ASN PRO ALA ILE ALA SEQRES 33 B 569 HIS GLY ILE SER GLU TYR VAL GLY SER VAL GLU VAL GLY SEQRES 34 B 569 LYS VAL ALA ASP LEU VAL LEU TRP SER PRO ALA PHE PHE SEQRES 35 B 569 GLY VAL LYS PRO ASN MET ILE ILE LYS GLY GLY PHE ILE SEQRES 36 B 569 ALA LEU SER GLN MET GLY ASP ALA ASN ALA SER ILE PRO SEQRES 37 B 569 THR PRO GLN PRO VAL TYR TYR ARG GLU MET PHE ALA HIS SEQRES 38 B 569 HIS GLY LYS ALA LYS TYR ASP ALA ASN ILE THR PHE VAL SEQRES 39 B 569 SER GLN ALA ALA TYR ASP LYS GLY ILE LYS GLU GLU LEU SEQRES 40 B 569 GLY LEU GLU ARG GLN VAL LEU PRO VAL LYS ASN CYS ARG SEQRES 41 B 569 ASN VAL THR LYS LYS ASP MET GLN PHE ASN ASN THR THR SEQRES 42 B 569 ALA HIS ILE GLU VAL ASN PRO GLU THR TYR HIS VAL PHE SEQRES 43 B 569 VAL ASP GLY LYS GLU VAL THR SER LYS PRO ALA ASN LYS SEQRES 44 B 569 VAL SER LEU ALA GLN LEU PHE SER ILE PHE MODRES 1E9Z KCX B 219 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX B 219 12 HET NI B3001 1 HET NI B3002 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM NI NICKEL (II) ION FORMUL 2 KCX C7 H14 N2 O4 FORMUL 3 NI 2(NI 2+) FORMUL 5 HOH *78(H2 O) HELIX 1 1 THR A 4 LYS A 26 1 23 HELIX 2 2 ASN A 31 ALA A 49 1 19 HELIX 3 3 THR A 53 GLY A 61 1 9 HELIX 4 4 ARG A 62 LEU A 64 5 3 HELIX 5 5 GLY A 73 ILE A 78 1 6 HELIX 6 6 HIS A 146 VAL A 150 5 5 HELIX 7 7 ASP A 157 PHE A 162 1 6 HELIX 8 8 ASP A 207 GLY A 222 1 16 HELIX 9 9 ARG B 6 GLY B 14 1 9 HELIX 10 10 LYS B 109 LEU B 112 5 4 HELIX 11 11 GLN B 143 GLY B 152 1 10 HELIX 12 12 ALA B 164 THR B 170 1 7 HELIX 13 13 PRO B 174 GLU B 187 1 14 HELIX 14 14 ASN B 203 ALA B 213 1 11 HELIX 15 15 ASP B 223 GLY B 225 5 3 HELIX 16 16 THR B 227 TYR B 241 1 15 HELIX 17 17 CYS B 257 ALA B 266 1 10 HELIX 18 18 PRO B 284 GLU B 292 5 9 HELIX 19 19 ASN B 309 MET B 315 1 7 HELIX 20 20 ASP B 316 CYS B 321 5 6 HELIX 21 21 GLU B 330 ALA B 335 1 6 HELIX 22 22 ARG B 340 MET B 353 1 14 HELIX 23 23 GLU B 371 GLY B 388 1 18 HELIX 24 24 ASP B 398 SER B 407 1 10 HELIX 25 25 THR B 410 HIS B 417 1 8 HELIX 26 26 SER B 438 PHE B 442 5 5 HELIX 27 27 PHE B 479 HIS B 482 5 4 HELIX 28 28 LYS B 484 ASN B 490 1 7 HELIX 29 29 SER B 495 GLY B 502 1 8 HELIX 30 30 GLY B 502 LEU B 507 1 6 HELIX 31 31 THR B 523 MET B 527 5 5 SHEET 1 AA 2 GLU A 80 PHE A 87 0 SHEET 2 AA 2 GLY A 90 HIS A 97 -1 O GLY A 90 N PHE A 87 SHEET 1 AB 2 ASP A 117 THR A 119 0 SHEET 2 AB 2 LYS B 3 SER B 5 -1 O ILE B 4 N ILE A 118 SHEET 1 AC 4 LEU A 154 ASP A 155 0 SHEET 2 AC 4 SER A 128 ASN A 133 -1 O LYS A 132 N ASP A 155 SHEET 3 AC 4 GLU A 181 ASP A 188 -1 O LYS A 182 N VAL A 131 SHEET 4 AC 4 LYS A 164 LEU A 166 -1 O ARG A 165 N ILE A 187 SHEET 1 AD 2 VAL A 139 GLY A 142 0 SHEET 2 AD 2 ALA A 173 PHE A 176 -1 O VAL A 174 N ILE A 141 SHEET 1 AE 2 ARG A 194 ILE A 195 0 SHEET 2 AE 2 ARG A 204 GLN A 205 -1 O ARG A 204 N ILE A 195 SHEET 1 BA 2 LYS B 20 ARG B 22 0 SHEET 2 BA 2 ILE B 29 GLU B 31 -1 O ALA B 30 N VAL B 21 SHEET 1 BB 8 LYS B 92 GLY B 97 0 SHEET 2 BB 8 GLY B 80 LYS B 89 -1 O ASP B 85 N GLY B 97 SHEET 3 BB 8 LEU B 68 ASP B 77 -1 O LEU B 68 N ILE B 88 SHEET 4 BB 8 ILE B 127 ALA B 130 1 O VAL B 128 N VAL B 76 SHEET 5 BB 8 LEU B 434 TRP B 437 -1 O VAL B 435 N THR B 129 SHEET 6 BB 8 MET B 448 LYS B 451 -1 O MET B 448 N LEU B 436 SHEET 7 BB 8 PHE B 454 MET B 460 -1 O PHE B 454 N LYS B 451 SHEET 8 BB 8 TYR B 474 GLU B 477 -1 O TYR B 474 N MET B 460 SHEET 1 BC 4 LYS B 92 GLY B 97 0 SHEET 2 BC 4 GLY B 80 LYS B 89 -1 O ASP B 85 N GLY B 97 SHEET 3 BC 4 LEU B 68 ASP B 77 -1 O LEU B 68 N ILE B 88 SHEET 4 BC 4 GLU B 119 ALA B 122 1 O GLU B 119 N ILE B 69 SHEET 1 BD 8 GLY B 132 HIS B 138 0 SHEET 2 BD 8 VAL B 153 GLY B 159 1 N THR B 154 O GLY B 132 SHEET 3 BD 8 ASN B 192 LYS B 198 1 O ASN B 192 N MET B 156 SHEET 4 BD 8 GLY B 217 HIS B 221 1 O GLY B 217 N ALA B 197 SHEET 5 BD 8 GLN B 244 HIS B 248 1 O GLN B 244 N PHE B 218 SHEET 6 BD 8 MET B 270 THR B 272 1 O HIS B 271 N ILE B 247 SHEET 7 BD 8 ILE B 295 SER B 299 1 O LEU B 296 N THR B 272 SHEET 8 BD 8 ILE B 358 THR B 359 1 O ILE B 358 N SER B 299 SHEET 1 BE 4 GLY B 132 HIS B 138 0 SHEET 2 BE 4 VAL B 153 GLY B 159 1 N THR B 154 O GLY B 132 SHEET 3 BE 4 ASN B 192 LYS B 198 1 O ASN B 192 N MET B 156 SHEET 4 BE 4 THR B 492 PHE B 493 -1 O PHE B 493 N PHE B 195 SHEET 1 BF 3 ILE B 536 VAL B 538 0 SHEET 2 BF 3 VAL B 545 VAL B 547 -1 O PHE B 546 N GLU B 537 SHEET 3 BF 3 LYS B 550 GLU B 551 -1 O LYS B 550 N VAL B 547 LINK C PHE B 218 N KCX B 219 1555 1555 1.32 LINK C KCX B 219 N ILE B 220 1555 1555 1.32 LINK NE2 HIS B 136 NI NI B3002 1555 1555 2.69 LINK NE2 HIS B 138 NI NI B3002 1555 1555 2.26 LINK OQ2 KCX B 219 NI NI B3001 1555 1555 2.74 LINK OQ2 KCX B 219 NI NI B3002 1555 1555 2.71 LINK ND1 HIS B 248 NI NI B3001 1555 1555 2.62 LINK NE2 HIS B 274 NI NI B3001 1555 1555 2.57 LINK OD1 ASP B 362 NI NI B3002 1555 1555 2.21 LINK O HOH B2027 NI NI B3001 1555 1555 2.62 LINK NI NI B3001 NI NI B3002 1555 1555 2.13 CISPEP 1 ALA B 283 PRO B 284 0 -0.06 CISPEP 2 ILE B 304 PRO B 305 0 -0.17 CISPEP 3 GLN B 471 PRO B 472 0 -0.11 SITE 1 AC1 7 KCX B 219 HIS B 221 HIS B 248 HIS B 274 SITE 2 AC1 7 ASP B 362 HOH B2027 NI B3002 SITE 1 AC2 5 HIS B 136 HIS B 138 KCX B 219 ASP B 362 SITE 2 AC2 5 NI B3001 CRYST1 177.910 177.910 177.910 90.00 90.00 90.00 I 2 3 24 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 0.005621 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005621 0.00000