PDB Short entry for 1KRC HEADER HYDROLASE (UREA AMIDO) 20-JUN-95 1KRC TITLE CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TITLE 2 TWO ACTIVE SITE MUTANTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.5; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UREASE; COMPND 8 CHAIN: B; COMPND 9 EC: 3.5.1.5; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: UREASE; COMPND 13 CHAIN: C; COMPND 14 EC: 3.5.1.5; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA AEROGENES; SOURCE 3 ORGANISM_TAXID: 28451; SOURCE 4 ORGAN: BEAN; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: KLEBSIELLA AEROGENES; SOURCE 7 ORGANISM_TAXID: 28451; SOURCE 8 ORGAN: BEAN; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: KLEBSIELLA AEROGENES; SOURCE 11 ORGANISM_TAXID: 28451; SOURCE 12 ORGAN: BEAN KEYWDS ACTIVE SITE MUTANT, NICKEL METALLOENZYME, HYDROLASE (UREA AMIDO) EXPDTA X-RAY DIFFRACTION AUTHOR E.JABRI,P.A.KARPLUS REVDAT 3 13-JUL-11 1KRC 1 VERSN REVDAT 2 24-FEB-09 1KRC 1 VERSN REVDAT 1 15-OCT-95 1KRC 0 JRNL AUTH E.JABRI,P.A.KARPLUS JRNL TITL STRUCTURES OF THE KLEBSIELLA AEROGENES UREASE APOENZYME AND JRNL TITL 2 TWO ACTIVE-SITE MUTANTS. JRNL REF BIOCHEMISTRY V. 35 10616 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8718850 JRNL DOI 10.1021/BI960424Z REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.JABRI,M.B.CARR,R.P.HAUSINGER,P.A.KARPLUS REMARK 1 TITL THE CRYSTAL STRUCTURE OF UREASE FROM KLEBSIELLA AEROGENES REMARK 1 REF SCIENCE V. 268 998 1995 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH I.-L.PARK,R.P.HAUSINGER REMARK 1 TITL SITE-DIRECTED MUTAGENESIS OF KLEBSIELLA AEROGENES UREASE: REMARK 1 TITL 2 IDENTIFICATION OF HISTIDINE RESIDUES THAT APPEAR TO FUNCTION REMARK 1 TITL 3 IN NICKEL LIGATION, SUBSTRATE BINDING, AND CATALYSIS REMARK 1 REF PROTEIN SCI. V. 2 1034 1993 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH E.JABRI,M.H.LEE,R.P.HAUSINGER,P.A.KARPLUS REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC STUDIES OF UREASE FROM JACK REMARK 1 TITL 2 BEAN AND FROM KLEBSIELLA AEROGENES REMARK 1 REF J.MOL.BIOL. V. 227 934 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 27755 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL 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 : 5779 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.20 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) : 0.25 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) : 1.88 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 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: REMARK 3 RESIDUES 308 - 330 IN CHAIN C HAVE HIGH B VALUES. THEY REMARK 3 CORRESPOND TO A MOBILE LOOP NEAR THE ACTIVE SITE. REMARK 4 REMARK 4 1KRC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE MARK II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28672 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 99.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y,-Z REMARK 290 16555 X,-Y,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z,-X,-Y+1/2 REMARK 290 19555 -Z,-X+1/2,Y REMARK 290 20555 -Z+1/2,X,-Y REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z,-X REMARK 290 23555 Y,-Z,-X+1/2 REMARK 290 24555 -Y,-Z+1/2,X 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 85.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 85.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 85.40000 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 85.40000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 85.40000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 85.40000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 85.40000 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 85.40000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 85.40000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 85.40000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 85.40000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 85.40000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 85.40000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 85.40000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 85.40000 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 85.40000 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 85.40000 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 85.40000 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 85.40000 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 85.40000 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 85.40000 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 85.40000 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 85.40000 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 85.40000 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 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 300 REMARK: THREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND REMARK 300 ALPHA (C) FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT REMARK 300 CONTAINS ONE (ABC)-UNIT. 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: NONAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: NONAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 48590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 55630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -315.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 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 GLU B 102 REMARK 465 VAL B 103 REMARK 465 ASN B 104 REMARK 465 ASP B 105 REMARK 465 GLU B 106 REMARK 465 MET C 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 PRO C 174 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 ASN C 299 N - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 LEU C 372 CA - CB - CG ANGL. DEV. = 14.0 DEGREES 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 ASN A 97 64.31 39.84 REMARK 500 ALA B 85 -146.69 -118.64 REMARK 500 PHE B 93 -128.39 59.96 REMARK 500 ALA C 24 -135.99 51.90 REMARK 500 LYS C 49 -168.26 -77.61 REMARK 500 MET C 55 -110.17 -108.24 REMARK 500 HIS C 272 64.52 27.23 REMARK 500 HIS C 280 123.62 -37.82 REMARK 500 MET C 317 -70.23 -177.10 REMARK 500 ALA C 320 0.33 -68.12 REMARK 500 SER C 359 -63.16 -98.40 REMARK 500 ASP C 360 52.06 87.79 REMARK 500 ALA C 363 55.88 -145.79 REMARK 500 MET C 364 48.10 81.81 REMARK 500 THR C 408 -92.94 -117.81 REMARK 500 VAL C 421 -166.69 -129.61 REMARK 500 HIS C 527 -1.26 67.39 REMARK 500 ALA C 561 -110.69 -131.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN C 299 21.2 L L OUTSIDE RANGE REMARK 500 GLN C 562 24.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 HOH 1, THE CATALYTIC WATER, BRIDGES THE TWO NICKEL IONS. REMARK 600 LYS 217 IS COVALENTLY MODIFIED AT NZ BY CO2. REMARK 600 REMARK 600 NI1 IS COORDINATED BY TWO NITROGENS (HIS 246 AND HIS 272) REMARK 600 AND TWO OXYGENS (LYS 217*) LIGANDS IN A PSEUDO-TETRAHEDRAL REMARK 600 GEOMETRY. NI2 IS COORDINATED BY TWO NITROGENS (HIS 134 REMARK 600 AND HIS 136) AND THREE OXYGENS (ASP 360, HOH 1, LYS 217*) REMARK 600 LIGANDS IN A ROUGHLY SQUARE PYRAMIDAL GEOMETRY. REMARK 600 1KAU= 2.2 ANGSTROM STRUCTURE-COMPLETE NICKEL COORDINATION REMARK 600 CONTAINS THE FULLY COORDINATED NICKEL METALLOCENTER. 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 C 574 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 272 NE2 REMARK 620 2 HOH C 577 O 116.8 REMARK 620 3 HIS C 246 ND1 95.7 136.4 REMARK 620 4 CO2 C 576 O1 105.7 107.2 89.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C 575 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CO2 C 576 O2 REMARK 620 2 HOH C 577 O 98.7 REMARK 620 3 ASP C 360 OD1 164.9 94.9 REMARK 620 4 HIS C 136 NE2 90.6 126.9 86.3 REMARK 620 5 HIS C 134 NE2 86.3 125.0 80.5 107.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: NIL REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: NICKEL METALLOCENTER REMARK 800 REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES IMPLICATED IN CATALYSIS REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 574 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 575 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO2 C 576 DBREF 1KRC A 1 100 UNP P18316 URE3_KLEAE 1 100 DBREF 1KRC B 1 106 UNP P18315 URE2_KLEAE 1 106 DBREF 1KRC C 1 567 UNP P18314 URE1_KLEAE 1 567 SEQADV 1KRC ALA C 320 UNP P18314 HIS 320 CONFLICT SEQRES 1 A 100 MET GLU LEU THR PRO ARG GLU LYS ASP LYS LEU LEU LEU SEQRES 2 A 100 PHE THR ALA ALA LEU VAL ALA GLU ARG ARG LEU ALA ARG SEQRES 3 A 100 GLY LEU LYS LEU ASN TYR PRO GLU SER VAL ALA LEU ILE SEQRES 4 A 100 SER ALA PHE ILE MET GLU GLY ALA ARG ASP GLY LYS SER SEQRES 5 A 100 VAL ALA SER LEU MET GLU GLU GLY ARG HIS VAL LEU THR SEQRES 6 A 100 ARG GLU GLN VAL MET GLU GLY VAL PRO GLU MET ILE PRO SEQRES 7 A 100 ASP ILE GLN VAL GLU ALA THR PHE PRO ASP GLY SER LYS SEQRES 8 A 100 LEU VAL THR VAL HIS ASN PRO ILE ILE SEQRES 1 B 106 MET ILE PRO GLY GLU TYR HIS VAL LYS PRO GLY GLN ILE SEQRES 2 B 106 ALA LEU ASN THR GLY ARG ALA THR CYS ARG VAL VAL VAL SEQRES 3 B 106 GLU ASN HIS GLY ASP ARG PRO ILE GLN VAL GLY SER HIS SEQRES 4 B 106 TYR HIS PHE ALA GLU VAL ASN PRO ALA LEU LYS PHE ASP SEQRES 5 B 106 ARG GLN GLN ALA ALA GLY TYR ARG LEU ASN ILE PRO ALA SEQRES 6 B 106 GLY THR ALA VAL ARG PHE GLU PRO GLY GLN LYS ARG GLU SEQRES 7 B 106 VAL GLU LEU VAL ALA PHE ALA GLY HIS ARG ALA VAL PHE SEQRES 8 B 106 GLY PHE ARG GLY GLU VAL MET GLY PRO LEU GLU VAL ASN SEQRES 9 B 106 ASP GLU SEQRES 1 C 567 MET SER ASN ILE SER ARG GLN ALA TYR ALA ASP MET PHE SEQRES 2 C 567 GLY PRO THR VAL GLY ASP LYS VAL ARG LEU ALA ASP THR SEQRES 3 C 567 GLU LEU TRP ILE GLU VAL GLU ASP ASP LEU THR THR TYR SEQRES 4 C 567 GLY GLU GLU VAL LYS PHE GLY GLY GLY LYS VAL ILE ARG SEQRES 5 C 567 ASP GLY MET GLY GLN GLY GLN MET LEU ALA ALA ASP CYS SEQRES 6 C 567 VAL ASP LEU VAL LEU THR ASN ALA LEU ILE VAL ASP HIS SEQRES 7 C 567 TRP GLY ILE VAL LYS ALA ASP ILE GLY VAL LYS ASP GLY SEQRES 8 C 567 ARG ILE PHE ALA ILE GLY LYS ALA GLY ASN PRO ASP ILE SEQRES 9 C 567 GLN PRO ASN VAL THR ILE PRO ILE GLY ALA ALA THR GLU SEQRES 10 C 567 VAL ILE ALA ALA GLU GLY LYS ILE VAL THR ALA GLY GLY SEQRES 11 C 567 ILE ASP THR HIS ILE HIS TRP ILE CYS PRO GLN GLN ALA SEQRES 12 C 567 GLU GLU ALA LEU VAL SER GLY VAL THR THR MET VAL GLY SEQRES 13 C 567 GLY GLY THR GLY PRO ALA ALA GLY THR HIS ALA THR THR SEQRES 14 C 567 CYS THR PRO GLY PRO TRP TYR ILE SER ARG MET LEU GLN SEQRES 15 C 567 ALA ALA ASP SER LEU PRO VAL ASN ILE GLY LEU LEU GLY SEQRES 16 C 567 LYS GLY ASN VAL SER GLN PRO ASP ALA LEU ARG GLU GLN SEQRES 17 C 567 VAL ALA ALA GLY VAL ILE GLY LEU LYS ILE HIS GLU ASP SEQRES 18 C 567 TRP GLY ALA THR PRO ALA ALA ILE ASP CYS ALA LEU THR SEQRES 19 C 567 VAL ALA ASP GLU MET ASP ILE GLN VAL ALA LEU HIS SER SEQRES 20 C 567 ASP THR LEU ASN GLU SER GLY PHE VAL GLU ASP THR LEU SEQRES 21 C 567 ALA ALA ILE GLY GLY ARG THR ILE HIS THR PHE HIS THR SEQRES 22 C 567 GLU GLY ALA GLY GLY GLY HIS ALA PRO ASP ILE ILE THR SEQRES 23 C 567 ALA CYS ALA HIS PRO ASN ILE LEU PRO SER SER THR ASN SEQRES 24 C 567 PRO THR LEU PRO TYR THR LEU ASN THR ILE ASP GLU HIS SEQRES 25 C 567 LEU ASP MET LEU MET VAL CYS ALA HIS LEU ASP PRO ASP SEQRES 26 C 567 ILE ALA GLU ASP VAL ALA PHE ALA GLU SER ARG ILE ARG SEQRES 27 C 567 ARG GLU THR ILE ALA ALA GLU ASP VAL LEU HIS ASP LEU SEQRES 28 C 567 GLY ALA PHE SER LEU THR SER SER ASP SER GLN ALA MET SEQRES 29 C 567 GLY ARG VAL GLY GLU VAL ILE LEU ARG THR TRP GLN VAL SEQRES 30 C 567 ALA HIS ARG MET LYS VAL GLN ARG GLY ALA LEU ALA GLU SEQRES 31 C 567 GLU THR GLY ASP ASN ASP ASN PHE ARG VAL LYS ARG TYR SEQRES 32 C 567 ILE ALA LYS TYR THR ILE ASN PRO ALA LEU THR HIS GLY SEQRES 33 C 567 ILE ALA HIS GLU VAL GLY SER ILE GLU VAL GLY LYS LEU SEQRES 34 C 567 ALA ASP LEU VAL VAL TRP SER PRO ALA PHE PHE GLY VAL SEQRES 35 C 567 LYS PRO ALA THR VAL ILE LYS GLY GLY MET ILE ALA ILE SEQRES 36 C 567 ALA PRO MET GLY ASP ILE ASN ALA SER ILE PRO THR PRO SEQRES 37 C 567 GLN PRO VAL HIS TYR ARG PRO MET PHE GLY ALA LEU GLY SEQRES 38 C 567 SER ALA ARG HIS HIS CYS ARG LEU THR PHE LEU SER GLN SEQRES 39 C 567 ALA ALA ALA ALA ASN GLY VAL ALA GLU ARG LEU ASN LEU SEQRES 40 C 567 ARG SER ALA ILE ALA VAL VAL LYS GLY CYS ARG THR VAL SEQRES 41 C 567 GLN LYS ALA ASP MET VAL HIS ASN SER LEU GLN PRO ASN SEQRES 42 C 567 ILE THR VAL ASP ALA GLN THR TYR GLU VAL ARG VAL ASP SEQRES 43 C 567 GLY GLU LEU ILE THR SER GLU PRO ALA ASP VAL LEU PRO SEQRES 44 C 567 MET ALA GLN ARG TYR PHE LEU PHE HET NI C 574 1 HET NI C 575 1 HET CO2 C 576 3 HETNAM NI NICKEL (II) ION HETNAM CO2 CARBON DIOXIDE FORMUL 4 NI 2(NI 2+) FORMUL 6 CO2 C O2 FORMUL 7 HOH *159(H2 O) HELIX 1 1 PRO A 5 ALA A 25 1 21 HELIX 2 2 TYR A 32 ASP A 49 1 18 HELIX 3 3 VAL A 53 HIS A 62 1 10 HELIX 4 4 ARG A 66 GLN A 68 5 3 HELIX 5 5 PRO A 74 MET A 76 5 3 HELIX 6 6 PHE B 42 GLU B 44 5 3 HELIX 7 7 ARG C 6 PHE C 13 1 8 HELIX 8 8 ALA C 62 ASP C 64 5 3 HELIX 9 9 PRO C 140 SER C 149 5 10 HELIX 10 10 ALA C 163 ALA C 167 1 5 HELIX 11 11 GLY C 173 SER C 186 1 14 HELIX 12 12 PRO C 202 ALA C 211 1 10 HELIX 13 13 GLU C 220 TRP C 222 5 3 HELIX 14 14 PRO C 226 MET C 239 1 14 HELIX 15 15 VAL C 256 ILE C 263 1 8 HELIX 16 16 ILE C 284 ALA C 289 5 6 HELIX 17 17 ASN C 299 THR C 301 5 3 HELIX 18 18 THR C 308 VAL C 318 1 11 HELIX 19 19 ALA C 327 ALA C 331 1 5 HELIX 20 20 ALA C 333 ARG C 336 1 4 HELIX 21 21 ARG C 339 LEU C 351 1 13 HELIX 22 22 VAL C 370 ARG C 385 1 16 HELIX 23 23 ASN C 397 TYR C 407 1 11 HELIX 24 24 ILE C 409 THR C 414 1 6 HELIX 25 25 PRO C 437 PHE C 439 5 3 HELIX 26 26 PHE C 477 ALA C 479 5 3 HELIX 27 27 GLY C 481 CYS C 487 1 7 HELIX 28 28 GLN C 494 ASN C 499 1 6 HELIX 29 29 VAL C 501 ARG C 504 1 4 HELIX 30 30 LYS C 522 ASP C 524 5 3 SHEET 1 A 2 ASP A 79 PHE A 86 0 SHEET 2 A 2 GLY A 89 HIS A 96 -1 N VAL A 95 O ILE A 80 SHEET 1 B 2 GLN B 12 ALA B 14 0 SHEET 2 B 2 ASN C 3 SER C 5 -1 N ILE C 4 O ILE B 13 SHEET 1 C 3 THR B 21 GLU B 27 0 SHEET 2 C 3 LYS B 76 ALA B 83 -1 N LEU B 81 O CYS B 22 SHEET 3 C 3 TYR B 59 LEU B 61 -1 N ARG B 60 O VAL B 82 SHEET 1 D 2 ILE B 34 GLY B 37 0 SHEET 2 D 2 ALA B 68 PHE B 71 -1 N PHE B 71 O ILE B 34 SHEET 1 E 2 LYS C 20 ARG C 22 0 SHEET 2 E 2 TRP C 29 GLU C 31 -1 N ILE C 30 O VAL C 21 SHEET 1 F 4 GLU C 117 ALA C 120 0 SHEET 2 F 4 LEU C 68 THR C 71 1 N VAL C 69 O GLU C 117 SHEET 3 F 4 ASP C 85 LYS C 89 -1 N VAL C 88 O LEU C 68 SHEET 4 F 4 ARG C 92 GLY C 97 -1 N GLY C 97 O ASP C 85 SHEET 1 G 2 ALA C 73 ASP C 77 0 SHEET 2 G 2 GLY C 80 ALA C 84 -1 N ALA C 84 O ALA C 73 SHEET 1 H 5 LYS C 124 ALA C 128 0 SHEET 2 H 5 LEU C 432 SER C 436 -1 N TRP C 435 O ILE C 125 SHEET 3 H 5 THR C 446 LYS C 449 -1 N ILE C 448 O LEU C 432 SHEET 4 H 5 MET C 452 MET C 458 -1 N ILE C 455 O VAL C 447 SHEET 5 H 5 HIS C 472 PRO C 475 -1 N ARG C 474 O ALA C 456 SHEET 1 I 3 ASN C 190 LEU C 193 0 SHEET 2 I 3 VAL C 151 GLY C 156 1 N MET C 154 O ASN C 190 SHEET 3 I 3 GLY C 130 ASP C 132 1 N GLY C 130 O THR C 152 SHEET 1 J 3 LEU C 194 LYS C 196 0 SHEET 2 J 3 GLY C 215 HIS C 219 1 N GLY C 215 O GLY C 195 SHEET 3 J 3 GLN C 242 HIS C 246 1 N GLN C 242 O LEU C 216 SHEET 1 K 2 ILE C 268 THR C 270 0 SHEET 2 K 2 ILE C 293 PRO C 295 1 N LEU C 294 O ILE C 268 SHEET 1 L 2 SER C 296 THR C 298 0 SHEET 2 L 2 LEU C 356 SER C 358 1 N LEU C 356 O SER C 297 SHEET 1 M 2 LEU C 489 LEU C 492 0 SHEET 2 M 2 ALA C 510 VAL C 513 1 N ALA C 510 O THR C 490 SHEET 1 N 2 ILE C 534 VAL C 536 0 SHEET 2 N 2 VAL C 543 VAL C 545 -1 N ARG C 544 O THR C 535 LINK NZ LYS C 217 C CO2 C 576 1555 1555 1.33 LINK NI NI C 574 NE2 HIS C 272 1555 1555 2.23 LINK NI NI C 574 O HOH C 577 1555 1555 2.33 LINK NI NI C 574 ND1 HIS C 246 1555 1555 2.11 LINK NI NI C 574 O1 CO2 C 576 1555 1555 2.09 LINK NI NI C 575 O2 CO2 C 576 1555 1555 2.17 LINK NI NI C 575 O HOH C 577 1555 1555 2.20 LINK NI NI C 575 OD1 ASP C 360 1555 1555 2.19 LINK NI NI C 575 NE2 HIS C 136 1555 1555 2.24 LINK NI NI C 575 NE2 HIS C 134 1555 1555 2.35 CISPEP 1 ALA C 281 PRO C 282 0 0.20 CISPEP 2 LEU C 302 PRO C 303 0 -0.99 CISPEP 3 GLN C 469 PRO C 470 0 0.37 SITE 1 NIL 9 HIS C 134 HIS C 136 LYS C 217 HIS C 246 SITE 2 NIL 9 HIS C 272 ASP C 360 NI C 574 NI C 575 SITE 3 NIL 9 MET A 1 SITE 1 ACT 2 HIS C 219 ALA C 320 SITE 1 AC1 7 HIS C 219 HIS C 246 HIS C 272 GLY C 277 SITE 2 AC1 7 NI C 575 CO2 C 576 HOH C 577 SITE 1 AC2 6 HIS C 134 HIS C 136 ASP C 360 NI C 574 SITE 2 AC2 6 CO2 C 576 HOH C 577 SITE 1 AC3 10 HIS C 134 HIS C 136 THR C 169 LYS C 217 SITE 2 AC3 10 HIS C 219 HIS C 246 PHE C 271 HIS C 272 SITE 3 AC3 10 NI C 574 NI C 575 CRYST1 170.800 170.800 170.800 90.00 90.00 90.00 I 21 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 0.005855 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005855 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005855 0.00000