HEADER HYDROLASE 09-SEP-13 3WIB TITLE CRYSTAL STRUCTURE OF Y109W MUTANT HALOALKANE DEHALOGENASE DATA FROM TITLE 2 AGROBACTERIUM TUMEFACIENS C58 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HALOALKANE DEHALOGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.8.1.5; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 176299; SOURCE 4 STRAIN: C58 / ATCC 33970; SOURCE 5 GENE: DHAA, DHA, ATU6064, AGR_PTI_130; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3) KEYWDS HALOALKANE DEHALOGENASE, HYDROLASE FOLD FAMILY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.J.GUAN,H.YABUKI,M.OKAI,J.OHTSUKA,M.TANOKURA REVDAT 2 24-AUG-22 3WIB 1 JRNL REMARK SEQADV REVDAT 1 23-JUL-14 3WIB 0 JRNL AUTH L.GUAN,H.YABUKI,M.OKAI,J.OHTSUKA,M.TANOKURA JRNL TITL CRYSTAL STRUCTURE OF THE NOVEL HALOALKANE DEHALOGENASE DATA JRNL TITL 2 FROM AGROBACTERIUM TUMEFACIENS C58 REVEALS A SPECIAL JRNL TITL 3 HALIDE-STABILIZING PAIR AND ENANTIOSELECTIVITY MECHANISM. JRNL REF APPL.MICROBIOL.BIOTECHNOL. V. 98 8573 2014 JRNL REFN ESSN 1432-0614 JRNL PMID 24770384 JRNL DOI 10.1007/S00253-014-5751-2 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 47662 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 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 : 2552 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3449 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 204 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : -0.40000 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): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.511 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4848 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4569 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6618 ; 1.786 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10467 ; 0.876 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 580 ; 6.305 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 241 ;34.014 ;23.112 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 731 ;12.960 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;16.739 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 716 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5516 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1213 ; 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): 2323 ; 2.386 ; 2.471 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2322 ; 2.385 ; 2.470 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2902 ; 3.149 ; 3.690 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2903 ; 3.149 ; 3.691 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2525 ; 2.824 ; 2.690 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2526 ; 2.823 ; 2.690 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3717 ; 4.211 ; 3.952 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5588 ; 5.337 ;19.935 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5529 ; 5.321 ;19.899 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3WIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000096370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50218 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M N-CYCLOHEXYL-2 REMARK 280 -AMINOETHANESULFONIC ACID (CHES), 1.0M POTASSIUM SODIUM TARTRATE, REMARK 280 0.2M LITHIUM SULFATE, 0.1M MANGANESE CHLORIDE, 1MM DTT, PH 8.5, REMARK 280 EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 2 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 MET A -5 REMARK 465 LYS A -4 REMARK 465 GLU A -3 REMARK 465 HIS A -2 REMARK 465 ARG A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 SER A 5 REMARK 465 ILE A 295 REMARK 465 ALA A 296 REMARK 465 GLY A 297 REMARK 465 ASN A 298 REMARK 465 MET B -5 REMARK 465 LYS B -4 REMARK 465 GLU B -3 REMARK 465 HIS B -2 REMARK 465 ARG B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLU B 3 REMARK 465 LYS B 4 REMARK 465 SER B 5 REMARK 465 GLY B 297 REMARK 465 ASN B 298 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 OD1 ASP A 235 NH2 ARG A 262 1.96 REMARK 500 OD2 ASP A 139 O HOH A 567 2.18 REMARK 500 O HOH B 476 O HOH B 484 2.18 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 18 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP B 67 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 155 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP B 214 CB - CG - OD1 ANGL. DEV. = 5.7 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 PRO A 44 57.09 -113.05 REMARK 500 THR A 45 -155.47 -110.18 REMARK 500 ASP A 98 72.82 41.46 REMARK 500 ASP A 108 -135.86 53.51 REMARK 500 GLU A 132 57.85 38.74 REMARK 500 LEU A 135 -41.69 -137.86 REMARK 500 GLU A 173 -59.50 -122.73 REMARK 500 PHE A 178 39.56 -90.07 REMARK 500 PHE A 247 -71.80 -152.13 REMARK 500 ILE A 273 -77.54 -103.65 REMARK 500 HIS A 274 -54.01 -134.46 REMARK 500 PHE B 22 41.35 35.17 REMARK 500 PRO B 44 56.14 -110.28 REMARK 500 THR B 45 -154.57 -113.01 REMARK 500 ASP B 108 -136.51 54.72 REMARK 500 GLU B 132 57.34 36.03 REMARK 500 LEU B 135 -40.74 -144.73 REMARK 500 GLU B 173 -65.18 -127.73 REMARK 500 PHE B 247 -74.64 -152.90 REMARK 500 ILE B 273 -77.08 -109.63 REMARK 500 HIS B 274 -54.23 -133.12 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 NHE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WI7 RELATED DB: PDB DBREF 3WIB A -5 298 UNP Q8U671 DHAA_AGRT5 1 304 DBREF 3WIB B -5 298 UNP Q8U671 DHAA_AGRT5 1 304 SEQADV 3WIB TRP A 109 UNP Q8U671 TYR 115 ENGINEERED MUTATION SEQADV 3WIB TRP B 109 UNP Q8U671 TYR 115 ENGINEERED MUTATION SEQRES 1 A 304 MET LYS GLU HIS ARG HIS MET THR GLU LYS SER PRO HIS SEQRES 2 A 304 SER ALA PHE GLY ASP GLY ALA LYS ALA TYR ASP VAL PRO SEQRES 3 A 304 ALA PHE GLY LEU GLN ILE HIS THR VAL GLU HIS GLY SER SEQRES 4 A 304 GLY ALA PRO ILE VAL PHE LEU HIS GLY ASN PRO THR SER SEQRES 5 A 304 SER TYR LEU TRP ARG HIS ILE PHE ARG ARG LEU HIS GLY SEQRES 6 A 304 HIS GLY ARG LEU LEU ALA VAL ASP LEU ILE GLY TYR GLY SEQRES 7 A 304 GLN SER SER LYS PRO ASP ILE GLU TYR THR LEU GLU ASN SEQRES 8 A 304 GLN GLN ARG TYR VAL ASP ALA TRP PHE ASP ALA LEU ASP SEQRES 9 A 304 LEU ARG ASN VAL THR LEU VAL LEU GLN ASP TRP GLY ALA SEQRES 10 A 304 ALA PHE GLY LEU ASN TRP ALA SER ARG ASN PRO ASP ARG SEQRES 11 A 304 VAL ARG ALA VAL ALA PHE PHE GLU PRO VAL LEU ARG ASN SEQRES 12 A 304 ILE ASP SER VAL ASP LEU SER PRO GLU PHE VAL THR ARG SEQRES 13 A 304 ARG ALA LYS LEU ARG GLN PRO GLY GLU GLY GLU ILE PHE SEQRES 14 A 304 VAL GLN GLN GLU ASN ARG PHE LEU THR GLU LEU PHE PRO SEQRES 15 A 304 TRP PHE PHE LEU THR PRO LEU ALA PRO GLU ASP LEU ARG SEQRES 16 A 304 GLN TYR GLN THR PRO PHE PRO THR PRO HIS SER ARG LYS SEQRES 17 A 304 ALA ILE LEU ALA GLY PRO ARG ASN LEU PRO VAL ASP GLY SEQRES 18 A 304 GLU PRO ALA SER THR VAL ALA PHE LEU GLU GLN ALA VAL SEQRES 19 A 304 ASN TRP LEU ASN THR SER ASP THR PRO LYS LEU LEU LEU SEQRES 20 A 304 THR PHE LYS PRO GLY PHE LEU LEU THR ASP ALA ILE LEU SEQRES 21 A 304 LYS TRP SER GLN VAL THR ILE ARG ASN LEU GLU ILE GLU SEQRES 22 A 304 ALA ALA GLY ALA GLY ILE HIS PHE VAL GLN GLU GLU GLN SEQRES 23 A 304 PRO GLU THR ILE ALA ARG LEU LEU ASP ALA TRP LEU THR SEQRES 24 A 304 ARG ILE ALA GLY ASN SEQRES 1 B 304 MET LYS GLU HIS ARG HIS MET THR GLU LYS SER PRO HIS SEQRES 2 B 304 SER ALA PHE GLY ASP GLY ALA LYS ALA TYR ASP VAL PRO SEQRES 3 B 304 ALA PHE GLY LEU GLN ILE HIS THR VAL GLU HIS GLY SER SEQRES 4 B 304 GLY ALA PRO ILE VAL PHE LEU HIS GLY ASN PRO THR SER SEQRES 5 B 304 SER TYR LEU TRP ARG HIS ILE PHE ARG ARG LEU HIS GLY SEQRES 6 B 304 HIS GLY ARG LEU LEU ALA VAL ASP LEU ILE GLY TYR GLY SEQRES 7 B 304 GLN SER SER LYS PRO ASP ILE GLU TYR THR LEU GLU ASN SEQRES 8 B 304 GLN GLN ARG TYR VAL ASP ALA TRP PHE ASP ALA LEU ASP SEQRES 9 B 304 LEU ARG ASN VAL THR LEU VAL LEU GLN ASP TRP GLY ALA SEQRES 10 B 304 ALA PHE GLY LEU ASN TRP ALA SER ARG ASN PRO ASP ARG SEQRES 11 B 304 VAL ARG ALA VAL ALA PHE PHE GLU PRO VAL LEU ARG ASN SEQRES 12 B 304 ILE ASP SER VAL ASP LEU SER PRO GLU PHE VAL THR ARG SEQRES 13 B 304 ARG ALA LYS LEU ARG GLN PRO GLY GLU GLY GLU ILE PHE SEQRES 14 B 304 VAL GLN GLN GLU ASN ARG PHE LEU THR GLU LEU PHE PRO SEQRES 15 B 304 TRP PHE PHE LEU THR PRO LEU ALA PRO GLU ASP LEU ARG SEQRES 16 B 304 GLN TYR GLN THR PRO PHE PRO THR PRO HIS SER ARG LYS SEQRES 17 B 304 ALA ILE LEU ALA GLY PRO ARG ASN LEU PRO VAL ASP GLY SEQRES 18 B 304 GLU PRO ALA SER THR VAL ALA PHE LEU GLU GLN ALA VAL SEQRES 19 B 304 ASN TRP LEU ASN THR SER ASP THR PRO LYS LEU LEU LEU SEQRES 20 B 304 THR PHE LYS PRO GLY PHE LEU LEU THR ASP ALA ILE LEU SEQRES 21 B 304 LYS TRP SER GLN VAL THR ILE ARG ASN LEU GLU ILE GLU SEQRES 22 B 304 ALA ALA GLY ALA GLY ILE HIS PHE VAL GLN GLU GLU GLN SEQRES 23 B 304 PRO GLU THR ILE ALA ARG LEU LEU ASP ALA TRP LEU THR SEQRES 24 B 304 ARG ILE ALA GLY ASN HET NHE A 401 13 HET NHE A 402 13 HET NHE B 301 13 HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 3 NHE 3(C8 H17 N O3 S) FORMUL 6 HOH *179(H2 O) HELIX 1 1 HIS A 7 GLY A 11 5 5 HELIX 2 2 SER A 46 LEU A 49 5 4 HELIX 3 3 TRP A 50 LEU A 57 1 8 HELIX 4 4 THR A 82 ASP A 98 1 17 HELIX 5 5 TRP A 109 ASN A 121 1 13 HELIX 6 6 ASP A 139 LEU A 143 5 5 HELIX 7 7 SER A 144 ARG A 155 1 12 HELIX 8 8 GLY A 158 GLN A 165 1 8 HELIX 9 9 ASN A 168 GLU A 173 1 6 HELIX 10 10 GLU A 173 PHE A 178 1 6 HELIX 11 11 ALA A 184 THR A 193 1 10 HELIX 12 12 PRO A 198 SER A 200 5 3 HELIX 13 13 ARG A 201 LEU A 211 1 11 HELIX 14 14 PRO A 217 GLN A 226 1 10 HELIX 15 15 ALA A 227 SER A 234 1 8 HELIX 16 16 THR A 250 ILE A 261 1 12 HELIX 17 17 PHE A 275 GLN A 280 1 6 HELIX 18 18 GLN A 280 ARG A 294 1 15 HELIX 19 19 HIS B 7 GLY B 11 5 5 HELIX 20 20 SER B 46 LEU B 49 5 4 HELIX 21 21 TRP B 50 LEU B 57 1 8 HELIX 22 22 THR B 82 ASP B 98 1 17 HELIX 23 23 TRP B 109 ASN B 121 1 13 HELIX 24 24 ASP B 139 LEU B 143 5 5 HELIX 25 25 SER B 144 GLN B 156 1 13 HELIX 26 26 GLY B 158 GLN B 165 1 8 HELIX 27 27 ASN B 168 GLU B 173 1 6 HELIX 28 28 GLU B 173 PHE B 178 1 6 HELIX 29 29 ALA B 184 THR B 193 1 10 HELIX 30 30 PRO B 198 SER B 200 5 3 HELIX 31 31 ARG B 201 LEU B 211 1 11 HELIX 32 32 PRO B 217 GLN B 226 1 10 HELIX 33 33 ALA B 227 SER B 234 1 8 HELIX 34 34 THR B 250 ILE B 261 1 12 HELIX 35 35 PHE B 275 GLU B 279 5 5 HELIX 36 36 GLN B 280 ALA B 296 1 17 SHEET 1 A 8 LYS A 15 ALA A 21 0 SHEET 2 A 8 LEU A 24 HIS A 31 -1 O GLU A 30 N LYS A 15 SHEET 3 A 8 ARG A 62 VAL A 66 -1 O LEU A 63 N HIS A 31 SHEET 4 A 8 PRO A 36 LEU A 40 1 N ILE A 37 O LEU A 64 SHEET 5 A 8 VAL A 102 ASP A 108 1 O VAL A 105 N VAL A 38 SHEET 6 A 8 VAL A 125 PRO A 133 1 O ALA A 129 N LEU A 104 SHEET 7 A 8 LYS A 238 PRO A 245 1 O LEU A 239 N PHE A 130 SHEET 8 A 8 LEU A 264 GLY A 272 1 O GLU A 265 N LYS A 238 SHEET 1 B 8 LYS B 15 ALA B 21 0 SHEET 2 B 8 LEU B 24 HIS B 31 -1 O LEU B 24 N ALA B 21 SHEET 3 B 8 ARG B 62 VAL B 66 -1 O ALA B 65 N VAL B 29 SHEET 4 B 8 PRO B 36 LEU B 40 1 N ILE B 37 O LEU B 64 SHEET 5 B 8 VAL B 102 ASP B 108 1 O VAL B 105 N VAL B 38 SHEET 6 B 8 VAL B 125 PRO B 133 1 O ALA B 129 N LEU B 104 SHEET 7 B 8 LYS B 238 PRO B 245 1 O LEU B 239 N PHE B 130 SHEET 8 B 8 LEU B 264 GLY B 272 1 O ALA B 269 N THR B 242 CISPEP 1 ASN A 43 PRO A 44 0 2.05 CISPEP 2 GLU A 216 PRO A 217 0 -1.37 CISPEP 3 LYS A 244 PRO A 245 0 -3.07 CISPEP 4 ASN B 43 PRO B 44 0 -0.35 CISPEP 5 GLU B 216 PRO B 217 0 -4.30 CISPEP 6 LYS B 244 PRO B 245 0 0.68 SITE 1 AC1 9 ASN A 43 ASP A 108 TRP A 109 PHE A 147 SITE 2 AC1 9 LEU A 174 GLY A 207 PRO A 208 PHE A 247 SITE 3 AC1 9 HIS A 274 SITE 1 AC2 8 TRP A 177 PHE A 179 PRO A 182 ILE A 273 SITE 2 AC2 8 HOH A 547 SER B 144 TRP B 177 PHE B 179 SITE 1 AC3 8 ASN B 43 ASP B 108 TRP B 109 PHE B 147 SITE 2 AC3 8 GLY B 207 PRO B 208 PHE B 247 HIS B 274 CRYST1 123.620 123.620 88.080 90.00 90.00 90.00 P 4 2 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 0.008089 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011353 0.00000