HEADER LYASE 31-JAN-11 2Y7E TITLE CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) TITLE 2 FROM CANDIDATUS CLOACAMONAS ACIDAMINOVORANS (TETRAGONAL FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 2-276; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDATUS CLOACAMONAS ACIDAMINOVORANS; SOURCE 3 ORGANISM_TAXID: 456827; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCRT7/CT-TOPO KEYWDS LYASE, ALDOLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.BELLINZONI,P.M.ALZARI REVDAT 4 20-DEC-23 2Y7E 1 REMARK LINK REVDAT 3 10-AUG-11 2Y7E 1 JRNL REMARK VERSN REVDAT 2 13-JUL-11 2Y7E 1 JRNL REMARK REVDAT 1 01-JUN-11 2Y7E 0 JRNL AUTH M.BELLINZONI,K.BASTARD,A.PERRET,A.ZAPARUCHA,N.PERCHAT, JRNL AUTH 2 C.VERGNE,T.WAGNER,R.C.DE MELO-MINARDI,F.ARTIGUENAVE, JRNL AUTH 3 G.N.COHEN,J.WEISSENBACH,M.SALANOUBAT,P.M.ALZARI JRNL TITL 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME: A COMMON FOLD FOR JRNL TITL 2 AN UNCOMMON CLAISEN-TYPE CONDENSATION. JRNL REF J.BIOL.CHEM. V. 286 27399 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21632536 JRNL DOI 10.1074/JBC.M111.253260 REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0093 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) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 126786 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6691 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) : 1.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7493 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 396 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4223 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 585 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.21000 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): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.145 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4413 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2997 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6012 ; 1.467 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7357 ; 0.938 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 579 ; 5.995 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 194 ;37.855 ;24.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 757 ;11.964 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.188 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 691 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4953 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 843 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 12314 ; 3.487 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 2 ; 7.631 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4315 ;10.789 ; 5.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2Y7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290047131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : CHANNEL CUT MONOCHROMATOR REMARK 200 CRYSTAL REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 133532 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2Y7D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.220 M MG FORMATE, 26.4% REMARK 280 GLYCEROL, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.53500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.09400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.09400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.80250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.09400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.09400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.26750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.09400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.09400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.80250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.09400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.09400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.26750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.53500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -199.2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.53500 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 ASN A 275 REMARK 465 LYS A 276 REMARK 465 MET B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 LYS B 276 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 1 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 GLU A 266 CG CD OE1 OE2 REMARK 470 HIS B -2 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 0 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 14 CG CD OE1 OE2 REMARK 470 ARG B 55 CG CD NE CZ NH1 NH2 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 O HOH A 2041 O HOH A 2122 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 76 CD GLU B 76 OE2 -0.078 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 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -3.4 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 THR A 11 -55.25 -130.40 REMARK 500 THR B 11 -55.91 -130.64 REMARK 500 ASP B 117 -168.98 -120.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2049 DISTANCE = 6.90 ANGSTROMS 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 46 NE2 REMARK 620 2 HIS A 48 NE2 97.4 REMARK 620 3 GLU A 230 OE2 100.0 95.4 REMARK 620 4 FMT A1275 O2 89.1 89.8 168.9 REMARK 620 5 HOH A2296 O 91.8 169.5 87.8 85.4 REMARK 620 6 HOH A2297 O 174.7 86.2 83.5 87.0 84.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1276 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2007 O REMARK 620 2 HOH A2008 O 88.6 REMARK 620 3 HOH A2009 O 92.9 177.7 REMARK 620 4 HOH A2025 O 92.3 89.4 92.2 REMARK 620 5 HOH A2115 O 89.4 92.0 86.3 177.8 REMARK 620 6 HOH A2268 O 175.3 86.9 91.5 89.0 89.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 46 NE2 REMARK 620 2 HIS B 48 NE2 96.8 REMARK 620 3 GLU B 230 OE2 100.5 93.0 REMARK 620 4 FMT B1276 O2 88.4 92.2 169.0 REMARK 620 5 HOH B2287 O 91.2 171.8 87.7 85.9 REMARK 620 6 HOH B2288 O 173.5 87.9 83.6 86.9 84.0 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1275 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1276 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y7D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME REMARK 900 (KCE) FROM CANDIDATUS CLOACAMONAS ACIDAMINOVORANS (ORTHOROMBIC FORM) REMARK 900 RELATED ID: 2Y7G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME REMARK 900 (KCE) FROM C. CLOACAMONAS ACIDAMINOVORANS IN COMPLEX WITH THE REMARK 900 PRODUCT ACETOACETATE REMARK 900 RELATED ID: 2Y7F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME REMARK 900 (KCE) FROM C. CLOACAMONAS ACIDAMINOVORANS IN COMPLEX WITH THE REMARK 900 SUBSTRATE 3-KETO-5-AMINOHEXANOATE DBREF 2Y7E A 2 276 UNP B0VHH0 B0VHH0_CLOAI 2 276 DBREF 2Y7E B 2 276 UNP B0VHH0 B0VHH0_CLOAI 2 276 SEQADV 2Y7E MET A -5 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS A -4 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS A -3 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS A -2 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS A -1 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS A 0 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS A 1 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E MET B -5 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS B -4 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS B -3 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS B -2 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS B -1 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS B 0 UNP B0VHH0 EXPRESSION TAG SEQADV 2Y7E HIS B 1 UNP B0VHH0 EXPRESSION TAG SEQRES 1 A 282 MET HIS HIS HIS HIS HIS HIS GLU PRO LEU ILE LEU THR SEQRES 2 A 282 ALA ALA ILE THR GLY ALA GLU THR THR ARG ALA ASP GLN SEQRES 3 A 282 PRO ASN LEU PRO ILE THR PRO GLU GLU GLN ALA LYS GLU SEQRES 4 A 282 ALA LYS ALA CYS PHE GLU ALA GLY ALA ARG VAL ILE HIS SEQRES 5 A 282 LEU HIS ILE ARG GLU ASP ASP GLY ARG PRO SER GLN ARG SEQRES 6 A 282 LEU ASP ARG PHE GLN GLU ALA ILE SER ALA ILE ARG GLU SEQRES 7 A 282 VAL VAL PRO GLU ILE ILE ILE GLN ILE SER THR GLY GLY SEQRES 8 A 282 ALA VAL GLY GLU SER PHE ASP LYS ARG LEU ALA PRO LEU SEQRES 9 A 282 ALA LEU LYS PRO GLU MET ALA THR LEU ASN ALA GLY THR SEQRES 10 A 282 LEU ASN PHE GLY ASP ASP ILE PHE ILE ASN HIS PRO ALA SEQRES 11 A 282 ASP ILE ILE ARG LEU ALA GLU ALA PHE LYS GLN TYR ASN SEQRES 12 A 282 VAL VAL PRO GLU VAL GLU VAL TYR GLU SER GLY MET VAL SEQRES 13 A 282 ASP ALA VAL ALA ARG LEU ILE LYS LYS GLY ILE ILE THR SEQRES 14 A 282 GLN ASN PRO LEU HIS ILE GLN PHE VAL LEU GLY VAL PRO SEQRES 15 A 282 GLY GLY MET SER GLY LYS PRO LYS ASN LEU MET TYR MET SEQRES 16 A 282 MET GLU HIS LEU LYS GLU GLU ILE PRO THR ALA THR TRP SEQRES 17 A 282 ALA VAL ALA GLY ILE GLY ARG TRP HIS ILE PRO THR SER SEQRES 18 A 282 LEU ILE ALA MET VAL THR GLY GLY HIS ILE ARG CYS GLY SEQRES 19 A 282 PHE GLU ASP ASN ILE PHE TYR HIS LYS GLY VAL ILE ALA SEQRES 20 A 282 GLU SER ASN ALA GLN LEU VAL ALA ARG LEU ALA ARG ILE SEQRES 21 A 282 ALA LYS GLU ILE GLY ARG PRO LEU ALA THR PRO GLU GLN SEQRES 22 A 282 ALA ARG GLU ILE LEU ALA LEU ASN LYS SEQRES 1 B 282 MET HIS HIS HIS HIS HIS HIS GLU PRO LEU ILE LEU THR SEQRES 2 B 282 ALA ALA ILE THR GLY ALA GLU THR THR ARG ALA ASP GLN SEQRES 3 B 282 PRO ASN LEU PRO ILE THR PRO GLU GLU GLN ALA LYS GLU SEQRES 4 B 282 ALA LYS ALA CYS PHE GLU ALA GLY ALA ARG VAL ILE HIS SEQRES 5 B 282 LEU HIS ILE ARG GLU ASP ASP GLY ARG PRO SER GLN ARG SEQRES 6 B 282 LEU ASP ARG PHE GLN GLU ALA ILE SER ALA ILE ARG GLU SEQRES 7 B 282 VAL VAL PRO GLU ILE ILE ILE GLN ILE SER THR GLY GLY SEQRES 8 B 282 ALA VAL GLY GLU SER PHE ASP LYS ARG LEU ALA PRO LEU SEQRES 9 B 282 ALA LEU LYS PRO GLU MET ALA THR LEU ASN ALA GLY THR SEQRES 10 B 282 LEU ASN PHE GLY ASP ASP ILE PHE ILE ASN HIS PRO ALA SEQRES 11 B 282 ASP ILE ILE ARG LEU ALA GLU ALA PHE LYS GLN TYR ASN SEQRES 12 B 282 VAL VAL PRO GLU VAL GLU VAL TYR GLU SER GLY MET VAL SEQRES 13 B 282 ASP ALA VAL ALA ARG LEU ILE LYS LYS GLY ILE ILE THR SEQRES 14 B 282 GLN ASN PRO LEU HIS ILE GLN PHE VAL LEU GLY VAL PRO SEQRES 15 B 282 GLY GLY MET SER GLY LYS PRO LYS ASN LEU MET TYR MET SEQRES 16 B 282 MET GLU HIS LEU LYS GLU GLU ILE PRO THR ALA THR TRP SEQRES 17 B 282 ALA VAL ALA GLY ILE GLY ARG TRP HIS ILE PRO THR SER SEQRES 18 B 282 LEU ILE ALA MET VAL THR GLY GLY HIS ILE ARG CYS GLY SEQRES 19 B 282 PHE GLU ASP ASN ILE PHE TYR HIS LYS GLY VAL ILE ALA SEQRES 20 B 282 GLU SER ASN ALA GLN LEU VAL ALA ARG LEU ALA ARG ILE SEQRES 21 B 282 ALA LYS GLU ILE GLY ARG PRO LEU ALA THR PRO GLU GLN SEQRES 22 B 282 ALA ARG GLU ILE LEU ALA LEU ASN LYS HET ZN A 301 1 HET FMT A1275 3 HET MG A1276 1 HET ZN B 301 1 HET FMT B1276 3 HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID HETNAM MG MAGNESIUM ION FORMUL 3 ZN 2(ZN 2+) FORMUL 4 FMT 2(C H2 O2) FORMUL 5 MG MG 2+ FORMUL 8 HOH *585(H2 O) HELIX 1 1 THR A 26 GLY A 41 1 16 HELIX 2 2 ARG A 59 VAL A 74 1 16 HELIX 3 3 SER A 90 ALA A 96 1 7 HELIX 4 4 PRO A 97 LYS A 101 5 5 HELIX 5 5 HIS A 122 TYR A 136 1 15 HELIX 6 6 GLU A 146 LYS A 159 1 14 HELIX 7 7 LYS A 182 ILE A 197 1 16 HELIX 8 8 TRP A 210 VAL A 220 1 11 HELIX 9 9 SER A 243 GLY A 259 1 17 HELIX 10 10 THR A 264 LEU A 272 1 9 HELIX 11 11 HIS B -2 GLU B 2 5 5 HELIX 12 12 THR B 26 GLY B 41 1 16 HELIX 13 13 ARG B 59 VAL B 74 1 16 HELIX 14 14 SER B 90 ALA B 96 1 7 HELIX 15 15 PRO B 97 LYS B 101 5 5 HELIX 16 16 HIS B 122 ASN B 137 1 16 HELIX 17 17 GLU B 146 LYS B 159 1 14 HELIX 18 18 LYS B 182 ILE B 197 1 16 HELIX 19 19 TRP B 210 VAL B 220 1 11 HELIX 20 20 SER B 243 GLY B 259 1 17 HELIX 21 21 THR B 264 LEU B 272 1 9 SHEET 1 AA 9 LEU A 6 ALA A 9 0 SHEET 2 AA 9 HIS A 224 CYS A 227 1 O ILE A 225 N THR A 7 SHEET 3 AA 9 THR A 201 GLY A 206 1 O TRP A 202 N HIS A 224 SHEET 4 AA 9 HIS A 168 LEU A 173 1 O ILE A 169 N ALA A 203 SHEET 5 AA 9 VAL A 139 VAL A 144 1 O PRO A 140 N HIS A 168 SHEET 6 AA 9 MET A 104 ASN A 108 1 O ALA A 105 N GLU A 141 SHEET 7 AA 9 ILE A 78 ILE A 81 1 O ILE A 79 N MET A 104 SHEET 8 AA 9 ALA A 42 LEU A 47 1 O ARG A 43 N ILE A 78 SHEET 9 AA 9 LEU A 6 ALA A 9 1 O LEU A 6 N ARG A 43 SHEET 1 AB 2 ILE A 49 ARG A 50 0 SHEET 2 AB 2 PRO A 56 SER A 57 -1 O SER A 57 N ILE A 49 SHEET 1 AC 2 LEU A 112 PHE A 114 0 SHEET 2 AC 2 ASP A 117 PHE A 119 -1 O ASP A 117 N PHE A 114 SHEET 1 AD 2 PHE A 234 HIS A 236 0 SHEET 2 AD 2 VAL A 239 ILE A 240 -1 O VAL A 239 N TYR A 235 SHEET 1 BA 9 LEU B 6 ALA B 9 0 SHEET 2 BA 9 HIS B 224 CYS B 227 1 O ILE B 225 N THR B 7 SHEET 3 BA 9 THR B 201 GLY B 206 1 O TRP B 202 N HIS B 224 SHEET 4 BA 9 HIS B 168 LEU B 173 1 O ILE B 169 N ALA B 203 SHEET 5 BA 9 VAL B 139 VAL B 144 1 O PRO B 140 N HIS B 168 SHEET 6 BA 9 MET B 104 ASN B 108 1 O ALA B 105 N GLU B 141 SHEET 7 BA 9 ILE B 78 ILE B 81 1 O ILE B 79 N MET B 104 SHEET 8 BA 9 ALA B 42 LEU B 47 1 O ARG B 43 N ILE B 78 SHEET 9 BA 9 LEU B 6 ALA B 9 1 O LEU B 6 N ARG B 43 SHEET 1 BB 2 ILE B 49 ARG B 50 0 SHEET 2 BB 2 PRO B 56 SER B 57 -1 O SER B 57 N ILE B 49 SHEET 1 BC 2 LEU B 112 PHE B 114 0 SHEET 2 BC 2 ASP B 117 PHE B 119 -1 O ASP B 117 N PHE B 114 SHEET 1 BD 2 PHE B 234 HIS B 236 0 SHEET 2 BD 2 VAL B 239 ILE B 240 -1 O VAL B 239 N TYR B 235 LINK NE2 HIS A 46 ZN ZN A 301 1555 1555 2.21 LINK NE2 HIS A 48 ZN ZN A 301 1555 1555 2.21 LINK OE2 GLU A 230 ZN ZN A 301 1555 1555 1.95 LINK ZN ZN A 301 O2 FMT A1275 1555 1555 2.08 LINK ZN ZN A 301 O HOH A2296 1555 1555 2.20 LINK ZN ZN A 301 O HOH A2297 1555 1555 2.24 LINK MG MG A1276 O HOH A2007 1555 1555 1.99 LINK MG MG A1276 O HOH A2008 1555 1555 2.06 LINK MG MG A1276 O HOH A2009 1555 1555 1.99 LINK MG MG A1276 O HOH A2025 1555 1555 2.10 LINK MG MG A1276 O HOH A2115 1555 1555 2.05 LINK MG MG A1276 O HOH A2268 1555 1555 2.20 LINK NE2 HIS B 46 ZN ZN B 301 1555 1555 2.22 LINK NE2 HIS B 48 ZN ZN B 301 1555 1555 2.22 LINK OE2 GLU B 230 ZN ZN B 301 1555 1555 1.96 LINK ZN ZN B 301 O2 FMT B1276 1555 1555 2.04 LINK ZN ZN B 301 O HOH B2287 1555 1555 2.19 LINK ZN ZN B 301 O HOH B2288 1555 1555 2.19 CISPEP 1 ASN A 165 PRO A 166 0 0.47 CISPEP 2 ASN B 165 PRO B 166 0 4.33 SITE 1 AC1 6 HIS A 46 HIS A 48 GLU A 230 FMT A1275 SITE 2 AC1 6 HOH A2296 HOH A2297 SITE 1 AC2 10 HIS A 46 HIS A 48 SER A 82 GLY A 84 SITE 2 AC2 10 THR A 106 ASN A 108 GLU A 143 ZN A 301 SITE 3 AC2 10 HOH A2296 HOH A2297 SITE 1 AC3 6 HOH A2007 HOH A2008 HOH A2009 HOH A2025 SITE 2 AC3 6 HOH A2115 HOH A2268 SITE 1 AC4 6 HIS B 46 HIS B 48 GLU B 230 FMT B1276 SITE 2 AC4 6 HOH B2287 HOH B2288 SITE 1 AC5 10 HIS B 46 HIS B 48 SER B 82 GLY B 84 SITE 2 AC5 10 THR B 106 ASN B 108 GLU B 143 ZN B 301 SITE 3 AC5 10 HOH B2287 HOH B2288 CRYST1 102.188 102.188 101.070 90.00 90.00 90.00 P 43 21 2 16 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 0.009786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009894 0.00000 MTRIX1 1 0.004300 0.990200 0.139500 -8.30550 1 MTRIX2 1 0.992100 -0.021800 0.123800 1.56030 1 MTRIX3 1 0.125600 0.137900 -0.982500 50.24940 1