HEADER HYDROLASE 01-FEB-05 1YQC TITLE CRYSTAL STRUCTURE OF UREIDOGLYCOLATE HYDROLASE (ALLA) FROM ESCHERICHIA TITLE 2 COLI O157:H7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREIDOGLYCOLATE HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.3.19; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 STRAIN: O157:H7; SOURCE 5 GENE: ALLA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET20B KEYWDS ALLA, UREIDOGLYCOLATE, HYDROLASE, PURINE METABOLISM, STRUCTURAL KEYWDS 2 GENOMICS, MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS KEYWDS 3 INITIATIVE, BSGI EXPDTA X-RAY DIFFRACTION AUTHOR S.RAYMOND,A.TOCILJ,A.MATTE,M.CYGLER,MONTREAL-KINGSTON BACTERIAL AUTHOR 2 STRUCTURAL GENOMICS INITIATIVE (BSGI) REVDAT 4 11-OCT-17 1YQC 1 REMARK REVDAT 3 13-JUL-11 1YQC 1 VERSN REVDAT 2 24-FEB-09 1YQC 1 VERSN REVDAT 1 18-OCT-05 1YQC 0 JRNL AUTH S.RAYMOND,A.TOCILJ,E.AJAMIAN,Y.LI,M.-N.HUNG,A.MATTE,M.CYGLER JRNL TITL CRYSTAL STRUCTURE OF UREIDOGLYCOLATE HYDROLASE (ALLA) FROM JRNL TITL 2 ESCHERICHIA COLI O157:H7 JRNL REF PROTEINS V. 61 454 2005 JRNL REFN ISSN 0887-3585 JRNL PMID 16114032 JRNL DOI 10.1002/PROT.20537 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.OTWINOWSKI,W.MINOR REMARK 1 TITL PROCESSING OF X-RAY DIFFRACTION DATA COLLECTED IN REMARK 1 TITL 2 OSCILLATION MODE REMARK 1 REF METHODS ENZYMOL. V. 276 307 1997 REMARK 1 REFN ISSN 0076-6879 REMARK 1 PMID 15488195 REMARK 1 DOI 10.1016/S0076-6879(04)90029-8 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.C.TERWILLIGER,J.BERENDZEN REMARK 1 TITL AUTOMATED MAD AND MIR STRUCTURE SOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 849 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10089316 REMARK 1 DOI 10.1107/S0907444999000839 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.C.TERWILLIGER REMARK 1 TITL MAXIMUM-LIKELIHOOD DENSITY MODIFICATION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 965 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10944333 REMARK 1 DOI 10.1107/S0907444900005072 REMARK 1 REFERENCE 4 REMARK 1 AUTH G.N.MURSHUDOV REMARK 1 TITL REFINEMENT OF MACROMOLECULAR STRUCTURES BY THE REMARK 1 TITL 2 MAXIMUM-LIKELIHOOD METHOD REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 53 240 1997 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15299926 REMARK 1 DOI 10.1107/S0907444996012255 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.710 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 35732 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.987 REMARK 3 FREE R VALUE TEST SET COUNT : 1782 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) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2610 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2554 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 319 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06400 REMARK 3 B22 (A**2) : 0.11600 REMARK 3 B33 (A**2) : -0.06200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2620 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3568 ; 1.760 ; 1.931 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 318 ; 6.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;37.353 ;24.638 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 420 ;17.345 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.348 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 400 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2046 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1315 ; 0.233 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1775 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 285 ; 0.171 ; 0.200 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): 35 ; 0.313 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.173 ; 0.200 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): 1643 ; 1.276 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2590 ; 1.888 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1090 ; 2.768 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 978 ; 4.091 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 160 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0776 43.2011 -0.4963 REMARK 3 T TENSOR REMARK 3 T11: -0.0190 T22: -0.0316 REMARK 3 T33: -0.0134 T12: -0.0128 REMARK 3 T13: 0.0118 T23: -0.0253 REMARK 3 L TENSOR REMARK 3 L11: 0.4716 L22: 0.4663 REMARK 3 L33: 1.6659 L12: 0.3360 REMARK 3 L13: 0.6865 L23: 0.3936 REMARK 3 S TENSOR REMARK 3 S11: -0.0362 S12: 0.0664 S13: -0.1539 REMARK 3 S21: -0.1035 S22: 0.1043 S23: -0.0032 REMARK 3 S31: -0.1582 S32: 0.0610 S33: -0.0682 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 160 REMARK 3 ORIGIN FOR THE GROUP (A): 7.4548 43.2255 24.3596 REMARK 3 T TENSOR REMARK 3 T11: -0.0214 T22: -0.0196 REMARK 3 T33: -0.0151 T12: 0.0196 REMARK 3 T13: 0.0141 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 0.5890 L22: 0.4037 REMARK 3 L33: 1.7243 L12: -0.4277 REMARK 3 L13: 0.8056 L23: -0.3442 REMARK 3 S TENSOR REMARK 3 S11: -0.0679 S12: -0.1182 S13: -0.1660 REMARK 3 S21: 0.0897 S22: 0.1362 S23: -0.0136 REMARK 3 S31: -0.1709 S32: -0.1496 S33: -0.0683 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1YQC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9611, 0.9800, 0.9802 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36248 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE 2.06, RESOLVE 2.06 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 37.23300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 GLY B 161 REMARK 465 SER B 162 REMARK 465 HIS B 163 REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 REMARK 465 HIS B 170 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 ARG A 132 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 146 CG OD1 ND2 REMARK 470 ARG B 132 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 146 CG OD1 ND2 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 GLN A 49 O HOH A 1156 2.08 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 140 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG B 37 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP B 40 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 101 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 140 CB - CG - OD2 ANGL. DEV. = 6.8 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 ASP A 50 5.56 -62.90 REMARK 500 HIS A 69 15.19 -151.63 REMARK 500 ASP A 97 -73.79 -67.32 REMARK 500 ASN A 121 0.25 80.76 REMARK 500 GLN A 131 -49.67 71.50 REMARK 500 ASN B 32 68.88 37.68 REMARK 500 HIS B 69 7.31 -151.58 REMARK 500 ASN B 121 -1.09 81.35 REMARK 500 GLN B 131 -38.05 72.84 REMARK 500 ASN B 146 41.79 37.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLV A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ALLA_O157 RELATED DB: TARGETDB DBREF 1YQC A 1 160 UNP P63486 ALLA_ECO57 1 160 DBREF 1YQC B 1 160 UNP P63486 ALLA_ECO57 1 160 SEQADV 1YQC MSE A 1 UNP P63486 MET 1 MODIFIED RESIDUE SEQADV 1YQC MSE A 84 UNP P63486 MET 84 MODIFIED RESIDUE SEQADV 1YQC GLY A 161 UNP P63486 EXPRESSION TAG SEQADV 1YQC SER A 162 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 163 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 164 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 165 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 166 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 167 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 168 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 169 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS A 170 UNP P63486 EXPRESSION TAG SEQADV 1YQC MSE B 1 UNP P63486 MET 1 MODIFIED RESIDUE SEQADV 1YQC MSE B 84 UNP P63486 MET 84 MODIFIED RESIDUE SEQADV 1YQC GLY B 161 UNP P63486 EXPRESSION TAG SEQADV 1YQC SER B 162 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 163 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 164 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 165 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 166 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 167 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 168 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 169 UNP P63486 EXPRESSION TAG SEQADV 1YQC HIS B 170 UNP P63486 EXPRESSION TAG SEQRES 1 A 170 MSE LYS LEU GLN VAL LEU PRO LEU SER GLN GLU ALA PHE SEQRES 2 A 170 SER ALA TYR GLY ASP VAL ILE GLU THR GLN GLN ARG ASP SEQRES 3 A 170 PHE PHE HIS ILE ASN ASN GLY LEU VAL GLU ARG TYR HIS SEQRES 4 A 170 ASP LEU ALA LEU VAL GLU ILE LEU GLU GLN ASP ARG THR SEQRES 5 A 170 LEU ILE SER ILE ASN ARG ALA GLN PRO ALA ASN LEU PRO SEQRES 6 A 170 LEU THR ILE HIS GLU LEU GLU ARG HIS PRO LEU GLY THR SEQRES 7 A 170 GLN ALA PHE ILE PRO MSE LYS GLY GLU VAL PHE VAL VAL SEQRES 8 A 170 VAL VAL ALA LEU GLY ASP ASP LYS PRO ASP LEU SER THR SEQRES 9 A 170 LEU ARG ALA PHE ILE THR ASN GLY GLU GLN GLY VAL ASN SEQRES 10 A 170 TYR HIS ARG ASN VAL TRP HIS HIS PRO LEU PHE ALA TRP SEQRES 11 A 170 GLN ARG VAL THR ASP PHE LEU THR ILE ASP ARG GLY GLY SEQRES 12 A 170 SER ASP ASN CYS ASP VAL GLU SER ILE PRO GLU GLN GLU SEQRES 13 A 170 LEU CYS PHE ALA GLY SER HIS HIS HIS HIS HIS HIS HIS SEQRES 14 A 170 HIS SEQRES 1 B 170 MSE LYS LEU GLN VAL LEU PRO LEU SER GLN GLU ALA PHE SEQRES 2 B 170 SER ALA TYR GLY ASP VAL ILE GLU THR GLN GLN ARG ASP SEQRES 3 B 170 PHE PHE HIS ILE ASN ASN GLY LEU VAL GLU ARG TYR HIS SEQRES 4 B 170 ASP LEU ALA LEU VAL GLU ILE LEU GLU GLN ASP ARG THR SEQRES 5 B 170 LEU ILE SER ILE ASN ARG ALA GLN PRO ALA ASN LEU PRO SEQRES 6 B 170 LEU THR ILE HIS GLU LEU GLU ARG HIS PRO LEU GLY THR SEQRES 7 B 170 GLN ALA PHE ILE PRO MSE LYS GLY GLU VAL PHE VAL VAL SEQRES 8 B 170 VAL VAL ALA LEU GLY ASP ASP LYS PRO ASP LEU SER THR SEQRES 9 B 170 LEU ARG ALA PHE ILE THR ASN GLY GLU GLN GLY VAL ASN SEQRES 10 B 170 TYR HIS ARG ASN VAL TRP HIS HIS PRO LEU PHE ALA TRP SEQRES 11 B 170 GLN ARG VAL THR ASP PHE LEU THR ILE ASP ARG GLY GLY SEQRES 12 B 170 SER ASP ASN CYS ASP VAL GLU SER ILE PRO GLU GLN GLU SEQRES 13 B 170 LEU CYS PHE ALA GLY SER HIS HIS HIS HIS HIS HIS HIS SEQRES 14 B 170 HIS MODRES 1YQC MSE A 1 MET SELENOMETHIONINE MODRES 1YQC MSE A 84 MET SELENOMETHIONINE MODRES 1YQC MSE B 1 MET SELENOMETHIONINE MODRES 1YQC MSE B 84 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 84 8 HET MSE B 1 8 HET MSE B 84 8 HET GLV A1001 5 HETNAM MSE SELENOMETHIONINE HETNAM GLV GLYOXYLIC ACID HETSYN GLV GLYOXALATE, GLYOXYLATE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 GLV C2 H2 O3 FORMUL 4 HOH *319(H2 O) HELIX 1 1 SER A 9 SER A 14 1 6 HELIX 2 2 GLU A 48 ARG A 51 5 4 HELIX 3 3 SER B 9 SER B 14 1 6 HELIX 4 4 ASP B 101 LEU B 105 5 5 SHEET 1 A 7 LYS A 2 PRO A 7 0 SHEET 2 A 7 ARG A 106 ILE A 109 1 O ALA A 107 N LEU A 6 SHEET 3 A 7 VAL A 90 ALA A 94 -1 N VAL A 93 O ARG A 106 SHEET 4 A 7 TRP A 123 HIS A 124 -1 O TRP A 123 N ALA A 94 SHEET 5 A 7 THR A 67 ARG A 73 -1 N GLU A 72 O HIS A 124 SHEET 6 A 7 ASP A 148 CYS A 158 -1 O GLN A 155 N ILE A 68 SHEET 7 A 7 LYS A 2 PRO A 7 1 N VAL A 5 O CYS A 158 SHEET 1 B 7 GLY A 17 ILE A 20 0 SHEET 2 B 7 GLY A 115 TYR A 118 -1 O GLY A 115 N ILE A 20 SHEET 3 B 7 GLN A 79 PRO A 83 -1 N GLN A 79 O TYR A 118 SHEET 4 B 7 THR A 134 ASP A 140 -1 O LEU A 137 N ILE A 82 SHEET 5 B 7 LEU A 53 ALA A 59 -1 N SER A 55 O THR A 138 SHEET 6 B 7 VAL B 35 LEU B 43 -1 O TYR B 38 N ILE A 56 SHEET 7 B 7 PHE B 27 ILE B 30 -1 N ILE B 30 O VAL B 35 SHEET 1 C 7 PHE A 27 ILE A 30 0 SHEET 2 C 7 VAL A 35 LEU A 43 -1 O VAL A 35 N ILE A 30 SHEET 3 C 7 LEU B 53 ALA B 59 -1 O ILE B 56 N TYR A 38 SHEET 4 C 7 THR B 134 ASP B 140 -1 O THR B 138 N SER B 55 SHEET 5 C 7 GLN B 79 PRO B 83 -1 N ILE B 82 O LEU B 137 SHEET 6 C 7 GLY B 115 TYR B 118 -1 O TYR B 118 N GLN B 79 SHEET 7 C 7 GLY B 17 ILE B 20 -1 N ILE B 20 O GLY B 115 SHEET 1 D 7 LYS B 2 PRO B 7 0 SHEET 2 D 7 ARG B 106 ILE B 109 1 O ILE B 109 N LEU B 6 SHEET 3 D 7 VAL B 90 ALA B 94 -1 N VAL B 93 O ARG B 106 SHEET 4 D 7 TRP B 123 HIS B 124 -1 O TRP B 123 N ALA B 94 SHEET 5 D 7 THR B 67 ARG B 73 -1 N GLU B 72 O HIS B 124 SHEET 6 D 7 ASP B 148 CYS B 158 -1 O GLN B 155 N ILE B 68 SHEET 7 D 7 LYS B 2 PRO B 7 1 N VAL B 5 O CYS B 158 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C PRO A 83 N MSE A 84 1555 1555 1.34 LINK C MSE A 84 N LYS A 85 1555 1555 1.34 LINK C MSE B 1 N LYS B 2 1555 1555 1.34 LINK C PRO B 83 N MSE B 84 1555 1555 1.34 LINK C MSE B 84 N LYS B 85 1555 1555 1.34 CISPEP 1 LEU A 64 PRO A 65 0 17.07 CISPEP 2 LEU B 64 PRO B 65 0 8.02 SITE 1 AC1 8 GLU A 72 GLN A 79 PHE A 81 PRO A 126 SITE 2 AC1 8 LEU A 127 HOH A1020 HOH A1088 HOH A1113 CRYST1 43.047 74.466 56.364 90.00 103.89 90.00 P 1 21 1 4 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 0.023230 0.000000 0.005746 0.00000 SCALE2 0.000000 0.013429 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018277 0.00000 HETATM 1 N MSE A 1 1.443 37.930 -21.825 1.00 35.25 N HETATM 2 CA MSE A 1 2.683 37.120 -21.926 1.00 34.89 C HETATM 3 C MSE A 1 2.986 36.268 -20.669 1.00 33.32 C HETATM 4 O MSE A 1 2.062 35.851 -19.959 1.00 32.27 O HETATM 5 CB MSE A 1 3.868 37.999 -22.345 1.00 36.74 C HETATM 6 CG MSE A 1 4.243 39.123 -21.417 1.00 38.90 C HETATM 7 SE MSE A 1 3.003 40.604 -21.405 1.00 53.58 SE HETATM 8 CE MSE A 1 4.369 42.063 -21.560 1.00 42.06 C