HEADER HYDROLASE 19-MAY-08 3D6J TITLE CRYSTAL STRUCTURE OF PUTATIVE HALOACID DEHALOGENASE-LIKE HYDROLASE TITLE 2 FROM BACTEROIDES FRAGILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE HALOACID DEHALOGENASE-LIKE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS NCTC 9343; SOURCE 3 ORGANISM_TAXID: 272559; SOURCE 4 STRAIN: BACTEROIDES FRAGILIS (STRAIN ATCC 25285 / NCTC 9343); SOURCE 5 GENE: BF0931; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MAGIC; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG19B KEYWDS BACTEROIDES FRAGILIS, HALOACID DEHALOGENASE-LIKE HYDROLASE, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST KEYWDS 3 CENTER FOR STRUCTURAL GENOMICS, MCSG, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,R.WU,G.COBB,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (MCSG) REVDAT 3 13-JUL-11 3D6J 1 VERSN REVDAT 2 24-FEB-09 3D6J 1 VERSN REVDAT 1 15-JUL-08 3D6J 0 JRNL AUTH C.CHANG,R.WU,G.COBB,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE HALOACID DEHALOGENASE-LIKE JRNL TITL 2 HYDROLASE FROM BACTEROIDES FRAGILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 18404 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1220 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1658 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.44000 REMARK 3 B22 (A**2) : 1.44000 REMARK 3 B33 (A**2) : -2.87000 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): 0.182 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.272 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1762 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2400 ; 1.525 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 226 ; 8.750 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;35.542 ;23.205 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 306 ;14.759 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;17.862 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 276 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1318 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 847 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1216 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 207 ; 0.180 ; 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): 29 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.174 ; 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): 1103 ; 0.740 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1749 ; 1.138 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 743 ; 2.021 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 643 ; 2.931 ; 4.500 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 16 REMARK 3 RESIDUE RANGE : A 88 A 136 REMARK 3 ORIGIN FOR THE GROUP (A): 0.6269 43.4623 81.4372 REMARK 3 T TENSOR REMARK 3 T11: -0.0139 T22: 0.0035 REMARK 3 T33: 0.0658 T12: 0.0352 REMARK 3 T13: -0.0385 T23: -0.0467 REMARK 3 L TENSOR REMARK 3 L11: 1.8490 L22: 2.6804 REMARK 3 L33: 2.7259 L12: 0.0997 REMARK 3 L13: 0.0885 L23: 0.3828 REMARK 3 S TENSOR REMARK 3 S11: -0.0449 S12: 0.0559 S13: 0.3375 REMARK 3 S21: -0.1319 S22: -0.1091 S23: 0.5282 REMARK 3 S31: -0.5110 S32: -0.1753 S33: 0.1540 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 : A 17 A 87 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1141 32.2150 91.1474 REMARK 3 T TENSOR REMARK 3 T11: -0.0980 T22: -0.0694 REMARK 3 T33: -0.0927 T12: -0.0185 REMARK 3 T13: -0.0243 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 0.8721 L22: 3.8098 REMARK 3 L33: 2.0011 L12: -0.9724 REMARK 3 L13: -0.1680 L23: -0.2157 REMARK 3 S TENSOR REMARK 3 S11: -0.0774 S12: -0.0244 S13: 0.0404 REMARK 3 S21: 0.2041 S22: 0.0214 S23: -0.1027 REMARK 3 S31: -0.0071 S32: 0.0715 S33: 0.0560 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 137 A 211 REMARK 3 ORIGIN FOR THE GROUP (A): -0.5692 31.0200 77.0962 REMARK 3 T TENSOR REMARK 3 T11: -0.1529 T22: -0.0276 REMARK 3 T33: -0.0389 T12: 0.0095 REMARK 3 T13: -0.0310 T23: -0.0962 REMARK 3 L TENSOR REMARK 3 L11: 0.9117 L22: 2.0009 REMARK 3 L33: 2.6228 L12: 0.2158 REMARK 3 L13: 0.3860 L23: 0.8975 REMARK 3 S TENSOR REMARK 3 S11: -0.0042 S12: 0.0095 S13: -0.0550 REMARK 3 S21: -0.0638 S22: -0.2388 S23: 0.4155 REMARK 3 S31: 0.0296 S32: -0.2114 S33: 0.2431 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3D6J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB047654. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18723 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.170 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SODIUM PHOSPHATE PH5.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 66.95650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.31000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.31000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.47825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.31000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.31000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 100.43475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.31000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.31000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.47825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.31000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.31000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 100.43475 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 66.95650 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MSE A 1 REMARK 465 SER A 212 REMARK 465 VAL A 213 REMARK 465 PRO A 214 REMARK 465 GLU A 215 REMARK 465 ASP A 216 REMARK 465 LYS A 217 REMARK 465 SER A 218 REMARK 465 GLY A 219 REMARK 465 CYS A 220 REMARK 465 PRO A 221 REMARK 465 LEU A 222 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 MSE A 124 O HOH A 475 2.14 REMARK 500 OE1 GLU A 72 O HOH A 470 2.19 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 PHE A 129 N - CA - C ANGL. DEV. = -17.9 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 PHE A 10 -71.02 -102.76 REMARK 500 THR A 13 -59.05 -120.40 REMARK 500 HIS A 123 -72.91 -128.63 REMARK 500 THR A 186 44.35 -79.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 128 PHE A 129 -96.76 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 TRP A 128 16.1 L L OUTSIDE RANGE 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 A 395 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 398 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 399 DISTANCE = 7.27 ANGSTROMS REMARK 525 HOH A 465 DISTANCE = 5.92 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 253 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC60104 RELATED DB: TARGETDB DBREF 3D6J A 1 222 UNP Q5LGR4 Q5LGR4_BACFN 1 222 SEQADV 3D6J SER A -2 UNP Q5LGR4 EXPRESSION TAG SEQADV 3D6J ASN A -1 UNP Q5LGR4 EXPRESSION TAG SEQADV 3D6J ALA A 0 UNP Q5LGR4 EXPRESSION TAG SEQRES 1 A 225 SER ASN ALA MSE LYS TYR THR VAL TYR LEU PHE ASP PHE SEQRES 2 A 225 ASP TYR THR LEU ALA ASP SER SER ARG GLY ILE VAL THR SEQRES 3 A 225 CYS PHE ARG SER VAL LEU GLU ARG HIS GLY TYR THR GLY SEQRES 4 A 225 ILE THR ASP ASP MSE ILE LYS ARG THR ILE GLY LYS THR SEQRES 5 A 225 LEU GLU GLU SER PHE SER ILE LEU THR GLY ILE THR ASP SEQRES 6 A 225 ALA ASP GLN LEU GLU SER PHE ARG GLN GLU TYR SER LYS SEQRES 7 A 225 GLU ALA ASP ILE TYR MSE ASN ALA ASN THR ILE LEU PHE SEQRES 8 A 225 PRO ASP THR LEU PRO THR LEU THR HIS LEU LYS LYS GLN SEQRES 9 A 225 GLY ILE ARG ILE GLY ILE ILE SER THR LYS TYR ARG PHE SEQRES 10 A 225 ARG ILE LEU SER PHE LEU ARG ASN HIS MSE PRO ASP ASP SEQRES 11 A 225 TRP PHE ASP ILE ILE ILE GLY GLY GLU ASP VAL THR HIS SEQRES 12 A 225 HIS LYS PRO ASP PRO GLU GLY LEU LEU LEU ALA ILE ASP SEQRES 13 A 225 ARG LEU LYS ALA CYS PRO GLU GLU VAL LEU TYR ILE GLY SEQRES 14 A 225 ASP SER THR VAL ASP ALA GLY THR ALA ALA ALA ALA GLY SEQRES 15 A 225 VAL SER PHE THR GLY VAL THR SER GLY MSE THR THR ALA SEQRES 16 A 225 GLN GLU PHE GLN ALA TYR PRO TYR ASP ARG ILE ILE SER SEQRES 17 A 225 THR LEU GLY GLN LEU ILE SER VAL PRO GLU ASP LYS SER SEQRES 18 A 225 GLY CYS PRO LEU MODRES 3D6J MSE A 41 MET SELENOMETHIONINE MODRES 3D6J MSE A 81 MET SELENOMETHIONINE MODRES 3D6J MSE A 124 MET SELENOMETHIONINE MODRES 3D6J MSE A 189 MET SELENOMETHIONINE HET MSE A 41 8 HET MSE A 81 8 HET MSE A 124 8 HET MSE A 189 8 HET PO4 A 251 5 HET PO4 A 252 5 HET GOL A 253 6 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *222(H2 O) HELIX 1 1 SER A 17 HIS A 32 1 16 HELIX 2 2 THR A 38 ARG A 44 1 7 HELIX 3 3 THR A 49 GLY A 59 1 11 HELIX 4 4 ASP A 62 MSE A 81 1 20 HELIX 5 5 ASN A 82 THR A 85 5 4 HELIX 6 6 ASP A 90 GLY A 102 1 13 HELIX 7 7 TYR A 112 ASN A 122 1 11 HELIX 8 8 GLY A 134 VAL A 138 5 5 HELIX 9 9 PRO A 145 LEU A 155 1 11 HELIX 10 10 CYS A 158 GLU A 160 5 3 HELIX 11 11 SER A 168 GLY A 179 1 12 HELIX 12 12 GLN A 193 TYR A 198 5 6 HELIX 13 13 THR A 206 ILE A 211 5 6 SHEET 1 A 6 ILE A 131 ILE A 133 0 SHEET 2 A 6 ARG A 104 ILE A 108 1 N ILE A 107 O ILE A 133 SHEET 3 A 6 VAL A 5 PHE A 8 1 N PHE A 8 O GLY A 106 SHEET 4 A 6 VAL A 162 GLY A 166 1 O LEU A 163 N LEU A 7 SHEET 5 A 6 SER A 181 VAL A 185 1 O SER A 181 N TYR A 164 SHEET 6 A 6 ARG A 202 ILE A 204 1 O ILE A 204 N GLY A 184 SHEET 1 B 2 ALA A 15 ASP A 16 0 SHEET 2 B 2 ILE A 86 LEU A 87 -1 O ILE A 86 N ASP A 16 LINK C ASP A 40 N MSE A 41 1555 1555 1.34 LINK C MSE A 41 N ILE A 42 1555 1555 1.32 LINK C TYR A 80 N MSE A 81 1555 1555 1.32 LINK C MSE A 81 N ASN A 82 1555 1555 1.33 LINK C HIS A 123 N MSE A 124 1555 1555 1.34 LINK C MSE A 124 N PRO A 125 1555 1555 1.35 LINK C GLY A 188 N MSE A 189 1555 1555 1.33 LINK C MSE A 189 N THR A 190 1555 1555 1.33 CISPEP 1 ASP A 126 ASP A 127 0 -15.81 CISPEP 2 LYS A 142 PRO A 143 0 7.51 SITE 1 AC1 8 ASP A 9 PHE A 10 ASP A 11 SER A 109 SITE 2 AC1 8 THR A 110 LYS A 142 HOH A 261 HOH A 401 SITE 1 AC2 9 GLU A 52 THR A 139 HIS A 140 HIS A 141 SITE 2 AC2 9 HOH A 297 HOH A 337 HOH A 355 HOH A 370 SITE 3 AC2 9 HOH A 405 SITE 1 AC3 6 ASN A 82 SER A 118 ASN A 122 HOH A 267 SITE 2 AC3 6 HOH A 369 HOH A 385 CRYST1 62.620 62.620 133.913 90.00 90.00 90.00 P 41 21 2 8 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 0.015969 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007468 0.00000