HEADER LYASE 07-FEB-00 1EF8 TITLE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLMALONYL COA DECARBOXYLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 4.1.1.41 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS METHYLMALONYL COA, DECARBOXYLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.M.BENNING,T.HALLER,J.A.GERLT,H.M.HOLDEN REVDAT 4 07-FEB-24 1EF8 1 REMARK LINK REVDAT 3 04-OCT-17 1EF8 1 REMARK REVDAT 2 24-FEB-09 1EF8 1 VERSN REVDAT 1 24-MAY-00 1EF8 0 JRNL AUTH M.M.BENNING,T.HALLER,J.A.GERLT,H.M.HOLDEN JRNL TITL NEW REACTIONS IN THE CROTONASE SUPERFAMILY: STRUCTURE OF JRNL TITL 2 METHYLMALONYL COA DECARBOXYLASE FROM ESCHERICHIA COLI. JRNL REF BIOCHEMISTRY V. 39 4630 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10769118 JRNL DOI 10.1021/BI9928896 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 72476 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 7212 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1800 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 81399 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5966 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 603 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.030 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 16.300; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.007 ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : 0.007 ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 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 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : STANDARD TNT GEOMETRY LIBRARY REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-98 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 9.0 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 : RIGAKU RU200 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 : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : FRAMBO REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72476 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.02300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.10400 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: NULL REMARK 200 SOFTWARE USED: HEAVY REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, 100 MM AMMONIUM SULFATE, 100 REMARK 280 MM CHES, 5 MM SODIUM AZIDE, PH 9.0, BATCH, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 65.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.15000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.70000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 26200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 52360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -155.0 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 -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 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 PRO A 72 REMARK 465 SER A 73 REMARK 465 GLY A 74 REMARK 465 GLY A 75 REMARK 465 ARG A 76 REMARK 465 HIS B 69 REMARK 465 GLU B 70 REMARK 465 LEU B 71 REMARK 465 PRO B 72 REMARK 465 SER B 73 REMARK 465 GLY B 74 REMARK 465 GLY B 75 REMARK 465 ARG B 76 REMARK 465 ILE C 68 REMARK 465 HIS C 69 REMARK 465 GLU C 70 REMARK 465 LEU C 71 REMARK 465 PRO C 72 REMARK 465 SER C 73 REMARK 465 GLY C 74 REMARK 465 GLY C 75 REMARK 465 ARG C 76 REMARK 465 ASP C 77 REMARK 465 PRO C 78 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 HIS A 69 CG ND1 CD2 CE1 NE2 REMARK 470 PHE B 227 CG CD1 CD2 CE1 CE2 CZ 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 47 CD GLU A 47 OE2 0.081 REMARK 500 GLU A 70 CD GLU A 70 OE2 0.068 REMARK 500 GLU A 159 CD GLU A 159 OE2 0.067 REMARK 500 GLU A 218 CD GLU A 218 OE2 0.085 REMARK 500 GLU A 252 CD GLU A 252 OE2 0.069 REMARK 500 GLU B 47 CD GLU B 47 OE2 0.067 REMARK 500 GLU B 104 CD GLU B 104 OE2 0.080 REMARK 500 GLU B 113 CD GLU B 113 OE2 0.072 REMARK 500 GLU B 186 CD GLU B 186 OE2 0.069 REMARK 500 GLU B 188 CD GLU B 188 OE2 0.071 REMARK 500 GLU B 200 CD GLU B 200 OE2 0.070 REMARK 500 GLU B 218 CD GLU B 218 OE2 0.076 REMARK 500 GLU B 226 CD GLU B 226 OE2 0.083 REMARK 500 GLU C 186 CD GLU C 186 OE2 0.071 REMARK 500 GLU C 218 CD GLU C 218 OE2 0.082 REMARK 500 GLU C 226 CD GLU C 226 OE2 0.079 REMARK 500 GLU C 241 CD GLU C 241 OE2 0.070 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 67 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 83 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 151 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 189 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP B 42 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP B 83 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 83 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG B 86 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 86 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 MET B 131 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 ASP B 151 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP B 151 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP B 189 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP C 82 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP C 82 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP C 119 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP C 119 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP C 151 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 PHE C 227 CB - CG - CD1 ANGL. DEV. = -5.0 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 12 -111.76 63.34 REMARK 500 TYR A 21 37.10 -144.17 REMARK 500 PRO A 96 7.13 -69.79 REMARK 500 ASP A 151 -57.73 -123.59 REMARK 500 ALA A 164 17.19 59.11 REMARK 500 ALA A 219 39.73 -64.34 REMARK 500 ASN B 12 -118.96 59.61 REMARK 500 TYR B 21 32.96 -152.04 REMARK 500 TYR B 81 -39.49 -39.90 REMARK 500 PRO B 96 10.41 -68.79 REMARK 500 ALA B 164 18.62 59.55 REMARK 500 ALA B 219 41.71 -64.03 REMARK 500 ASN C 12 -119.44 62.93 REMARK 500 TYR C 21 31.66 -153.01 REMARK 500 PRO C 96 8.90 -68.47 REMARK 500 ALA C 219 46.42 -65.84 REMARK 500 GLU C 252 4.90 -69.38 REMARK 500 LYS C 253 58.66 38.06 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 300 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 220 NE2 REMARK 620 2 HIS B 220 NE2 99.9 REMARK 620 3 HIS C 220 NE2 99.6 102.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EF9 RELATED DB: PDB DBREF 1EF8 A 1 261 UNP P52045 MMCD_ECOLI 1 261 DBREF 1EF8 B 1 261 UNP P52045 MMCD_ECOLI 1 261 DBREF 1EF8 C 1 261 UNP P52045 MMCD_ECOLI 1 261 SEQRES 1 A 261 MET SER TYR GLN TYR VAL ASN VAL VAL THR ILE ASN LYS SEQRES 2 A 261 VAL ALA VAL ILE GLU PHE ASN TYR GLY ARG LYS LEU ASN SEQRES 3 A 261 ALA LEU SER LYS VAL PHE ILE ASP ASP LEU MET GLN ALA SEQRES 4 A 261 LEU SER ASP LEU ASN ARG PRO GLU ILE ARG CYS ILE ILE SEQRES 5 A 261 LEU ARG ALA PRO SER GLY SER LYS VAL PHE SER ALA GLY SEQRES 6 A 261 HIS ASP ILE HIS GLU LEU PRO SER GLY GLY ARG ASP PRO SEQRES 7 A 261 LEU SER TYR ASP ASP PRO LEU ARG GLN ILE THR ARG MET SEQRES 8 A 261 ILE GLN LYS PHE PRO LYS PRO ILE ILE SER MET VAL GLU SEQRES 9 A 261 GLY SER VAL TRP GLY GLY ALA PHE GLU MET ILE MET SER SEQRES 10 A 261 SER ASP LEU ILE ILE ALA ALA SER THR SER THR PHE SER SEQRES 11 A 261 MET THR PRO VAL ASN LEU GLY VAL PRO TYR ASN LEU VAL SEQRES 12 A 261 GLY ILE HIS ASN LEU THR ARG ASP ALA GLY PHE HIS ILE SEQRES 13 A 261 VAL LYS GLU LEU ILE PHE THR ALA SER PRO ILE THR ALA SEQRES 14 A 261 GLN ARG ALA LEU ALA VAL GLY ILE LEU ASN HIS VAL VAL SEQRES 15 A 261 GLU VAL GLU GLU LEU GLU ASP PHE THR LEU GLN MET ALA SEQRES 16 A 261 HIS HIS ILE SER GLU LYS ALA PRO LEU ALA ILE ALA VAL SEQRES 17 A 261 ILE LYS GLU GLU LEU ARG VAL LEU GLY GLU ALA HIS THR SEQRES 18 A 261 MET ASN SER ASP GLU PHE GLU ARG ILE GLN GLY MET ARG SEQRES 19 A 261 ARG ALA VAL TYR ASP SER GLU ASP TYR GLN GLU GLY MET SEQRES 20 A 261 ASN ALA PHE LEU GLU LYS ARG LYS PRO ASN PHE VAL GLY SEQRES 21 A 261 HIS SEQRES 1 B 261 MET SER TYR GLN TYR VAL ASN VAL VAL THR ILE ASN LYS SEQRES 2 B 261 VAL ALA VAL ILE GLU PHE ASN TYR GLY ARG LYS LEU ASN SEQRES 3 B 261 ALA LEU SER LYS VAL PHE ILE ASP ASP LEU MET GLN ALA SEQRES 4 B 261 LEU SER ASP LEU ASN ARG PRO GLU ILE ARG CYS ILE ILE SEQRES 5 B 261 LEU ARG ALA PRO SER GLY SER LYS VAL PHE SER ALA GLY SEQRES 6 B 261 HIS ASP ILE HIS GLU LEU PRO SER GLY GLY ARG ASP PRO SEQRES 7 B 261 LEU SER TYR ASP ASP PRO LEU ARG GLN ILE THR ARG MET SEQRES 8 B 261 ILE GLN LYS PHE PRO LYS PRO ILE ILE SER MET VAL GLU SEQRES 9 B 261 GLY SER VAL TRP GLY GLY ALA PHE GLU MET ILE MET SER SEQRES 10 B 261 SER ASP LEU ILE ILE ALA ALA SER THR SER THR PHE SER SEQRES 11 B 261 MET THR PRO VAL ASN LEU GLY VAL PRO TYR ASN LEU VAL SEQRES 12 B 261 GLY ILE HIS ASN LEU THR ARG ASP ALA GLY PHE HIS ILE SEQRES 13 B 261 VAL LYS GLU LEU ILE PHE THR ALA SER PRO ILE THR ALA SEQRES 14 B 261 GLN ARG ALA LEU ALA VAL GLY ILE LEU ASN HIS VAL VAL SEQRES 15 B 261 GLU VAL GLU GLU LEU GLU ASP PHE THR LEU GLN MET ALA SEQRES 16 B 261 HIS HIS ILE SER GLU LYS ALA PRO LEU ALA ILE ALA VAL SEQRES 17 B 261 ILE LYS GLU GLU LEU ARG VAL LEU GLY GLU ALA HIS THR SEQRES 18 B 261 MET ASN SER ASP GLU PHE GLU ARG ILE GLN GLY MET ARG SEQRES 19 B 261 ARG ALA VAL TYR ASP SER GLU ASP TYR GLN GLU GLY MET SEQRES 20 B 261 ASN ALA PHE LEU GLU LYS ARG LYS PRO ASN PHE VAL GLY SEQRES 21 B 261 HIS SEQRES 1 C 261 MET SER TYR GLN TYR VAL ASN VAL VAL THR ILE ASN LYS SEQRES 2 C 261 VAL ALA VAL ILE GLU PHE ASN TYR GLY ARG LYS LEU ASN SEQRES 3 C 261 ALA LEU SER LYS VAL PHE ILE ASP ASP LEU MET GLN ALA SEQRES 4 C 261 LEU SER ASP LEU ASN ARG PRO GLU ILE ARG CYS ILE ILE SEQRES 5 C 261 LEU ARG ALA PRO SER GLY SER LYS VAL PHE SER ALA GLY SEQRES 6 C 261 HIS ASP ILE HIS GLU LEU PRO SER GLY GLY ARG ASP PRO SEQRES 7 C 261 LEU SER TYR ASP ASP PRO LEU ARG GLN ILE THR ARG MET SEQRES 8 C 261 ILE GLN LYS PHE PRO LYS PRO ILE ILE SER MET VAL GLU SEQRES 9 C 261 GLY SER VAL TRP GLY GLY ALA PHE GLU MET ILE MET SER SEQRES 10 C 261 SER ASP LEU ILE ILE ALA ALA SER THR SER THR PHE SER SEQRES 11 C 261 MET THR PRO VAL ASN LEU GLY VAL PRO TYR ASN LEU VAL SEQRES 12 C 261 GLY ILE HIS ASN LEU THR ARG ASP ALA GLY PHE HIS ILE SEQRES 13 C 261 VAL LYS GLU LEU ILE PHE THR ALA SER PRO ILE THR ALA SEQRES 14 C 261 GLN ARG ALA LEU ALA VAL GLY ILE LEU ASN HIS VAL VAL SEQRES 15 C 261 GLU VAL GLU GLU LEU GLU ASP PHE THR LEU GLN MET ALA SEQRES 16 C 261 HIS HIS ILE SER GLU LYS ALA PRO LEU ALA ILE ALA VAL SEQRES 17 C 261 ILE LYS GLU GLU LEU ARG VAL LEU GLY GLU ALA HIS THR SEQRES 18 C 261 MET ASN SER ASP GLU PHE GLU ARG ILE GLN GLY MET ARG SEQRES 19 C 261 ARG ALA VAL TYR ASP SER GLU ASP TYR GLN GLU GLY MET SEQRES 20 C 261 ASN ALA PHE LEU GLU LYS ARG LYS PRO ASN PHE VAL GLY SEQRES 21 C 261 HIS HET NI A 300 1 HETNAM NI NICKEL (II) ION FORMUL 4 NI NI 2+ FORMUL 5 HOH *603(H2 O) HELIX 1 1 TYR A 21 LEU A 25 5 5 HELIX 2 2 SER A 29 LEU A 43 1 15 HELIX 3 3 ASP A 83 PHE A 95 1 13 HELIX 4 4 GLY A 109 SER A 118 1 10 HELIX 5 5 THR A 132 GLY A 137 1 6 HELIX 6 6 ASN A 141 ASN A 147 1 7 HELIX 7 7 GLY A 153 ALA A 164 1 12 HELIX 8 8 ALA A 169 VAL A 175 1 7 HELIX 9 9 GLU A 183 GLU A 185 5 3 HELIX 10 10 GLU A 186 SER A 199 1 14 HELIX 11 11 ALA A 202 ALA A 219 1 18 HELIX 12 12 ASN A 223 ASP A 239 1 17 HELIX 13 13 SER A 240 GLU A 252 1 13 HELIX 14 14 TYR B 21 LEU B 25 5 5 HELIX 15 15 SER B 29 LEU B 43 1 15 HELIX 16 16 ASP B 83 PHE B 95 1 13 HELIX 17 17 GLY B 109 SER B 118 1 10 HELIX 18 18 THR B 132 GLY B 137 1 6 HELIX 19 19 ASN B 141 ASN B 147 1 7 HELIX 20 20 GLY B 153 ALA B 164 1 12 HELIX 21 21 ALA B 169 VAL B 175 1 7 HELIX 22 22 GLU B 183 SER B 199 1 17 HELIX 23 23 ALA B 202 ALA B 219 1 18 HELIX 24 24 ASN B 223 ASP B 239 1 17 HELIX 25 25 SER B 240 GLU B 252 1 13 HELIX 26 26 TYR C 21 LEU C 25 5 5 HELIX 27 27 SER C 29 LEU C 43 1 15 HELIX 28 28 ASP C 83 PHE C 95 1 13 HELIX 29 29 GLY C 109 SER C 118 1 10 HELIX 30 30 THR C 132 GLY C 137 1 6 HELIX 31 31 ASN C 141 ASN C 147 1 7 HELIX 32 32 GLY C 153 ALA C 164 1 12 HELIX 33 33 ALA C 169 VAL C 175 1 7 HELIX 34 34 GLU C 183 SER C 199 1 17 HELIX 35 35 ALA C 202 ALA C 219 1 18 HELIX 36 36 ASN C 223 ASP C 239 1 17 HELIX 37 37 SER C 240 GLU C 252 1 13 SHEET 1 A 6 VAL A 6 ILE A 11 0 SHEET 2 A 6 VAL A 14 PHE A 19 -1 O VAL A 14 N ILE A 11 SHEET 3 A 6 CYS A 50 ARG A 54 1 O CYS A 50 N ALA A 15 SHEET 4 A 6 ILE A 99 VAL A 103 1 O ILE A 100 N LEU A 53 SHEET 5 A 6 LEU A 120 ALA A 124 1 O LEU A 120 N SER A 101 SHEET 6 A 6 HIS A 180 VAL A 182 1 O HIS A 180 N ALA A 123 SHEET 1 B 4 VAL A 61 SER A 63 0 SHEET 2 B 4 SER A 106 TRP A 108 1 O SER A 106 N SER A 63 SHEET 3 B 4 THR A 128 SER A 130 1 O THR A 128 N VAL A 107 SHEET 4 B 4 ILE A 167 THR A 168 -1 O ILE A 167 N PHE A 129 SHEET 1 C 6 VAL B 6 ILE B 11 0 SHEET 2 C 6 VAL B 14 PHE B 19 -1 O VAL B 14 N ILE B 11 SHEET 3 C 6 CYS B 50 ARG B 54 1 O CYS B 50 N ALA B 15 SHEET 4 C 6 ILE B 99 VAL B 103 1 N ILE B 100 O ILE B 51 SHEET 5 C 6 LEU B 120 ALA B 124 1 O LEU B 120 N SER B 101 SHEET 6 C 6 HIS B 180 VAL B 182 1 O HIS B 180 N ALA B 123 SHEET 1 D 4 VAL B 61 SER B 63 0 SHEET 2 D 4 SER B 106 TRP B 108 1 O SER B 106 N PHE B 62 SHEET 3 D 4 THR B 128 SER B 130 1 O THR B 128 N VAL B 107 SHEET 4 D 4 ILE B 167 THR B 168 -1 N ILE B 167 O PHE B 129 SHEET 1 E 6 VAL C 6 ILE C 11 0 SHEET 2 E 6 VAL C 14 PHE C 19 -1 O VAL C 14 N ILE C 11 SHEET 3 E 6 CYS C 50 ARG C 54 1 O CYS C 50 N ALA C 15 SHEET 4 E 6 ILE C 99 VAL C 103 1 N ILE C 100 O ILE C 51 SHEET 5 E 6 LEU C 120 ALA C 124 1 O LEU C 120 N SER C 101 SHEET 6 E 6 HIS C 180 VAL C 182 1 O HIS C 180 N ALA C 123 SHEET 1 F 4 VAL C 61 SER C 63 0 SHEET 2 F 4 SER C 106 TRP C 108 1 O SER C 106 N PHE C 62 SHEET 3 F 4 THR C 128 SER C 130 1 O THR C 128 N VAL C 107 SHEET 4 F 4 ILE C 167 THR C 168 -1 N ILE C 167 O PHE C 129 LINK NE2 HIS A 220 NI NI A 300 1555 1555 2.09 LINK NI NI A 300 NE2 HIS B 220 1555 1555 2.16 LINK NI NI A 300 NE2 HIS C 220 1555 1555 1.97 SITE 1 AC1 3 HIS A 220 HIS B 220 HIS C 220 CRYST1 130.300 115.400 80.300 90.00 127.80 90.00 C 1 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007675 0.000000 0.005953 0.00000 SCALE2 0.000000 0.008666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015761 0.00000