HEADER TRANSFERASE 28-SEP-18 6HRV TITLE CRYSTAL STRUCTURE OF THE ZEBRAFISH PEROXISOMAL SCP2-THIOLASE (TYPE-1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCP2-THIOLASE (TYPE-1); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STEROL CARRIER PROTEIN 2A; COMPND 5 EC: 2.3.1.176; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SCP2-THIOLASE (TYPE-1); COMPND 9 CHAIN: B; COMPND 10 SYNONYM: STEROL CARRIER PROTEIN 2A; COMPND 11 EC: 2.3.1.176; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: SCP2A, SCP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PGRO7; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGS21A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 13 ORGANISM_COMMON: ZEBRAFISH; SOURCE 14 ORGANISM_TAXID: 7955; SOURCE 15 GENE: SCP2A, SCP2; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_VARIANT: PGRO7; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PGS21A KEYWDS FATTY ACID METABOLISM, BILE ACID BIOSYNTHESIS, PEROXISOMAL BETA- KEYWDS 2 OXIDATION, THIOLYTIC CLEAVAGE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.WIERENGA,T.R.KIEMA,C.J.THAPA REVDAT 4 24-JAN-24 6HRV 1 REMARK REVDAT 3 13-FEB-19 6HRV 1 JRNL REVDAT 2 06-FEB-19 6HRV 1 JRNL REVDAT 1 02-JAN-19 6HRV 0 JRNL AUTH T.R.KIEMA,C.J.THAPA,M.LAITAOJA,W.SCHMITZ,M.M.MAKSIMAINEN, JRNL AUTH 2 T.FUKAO,J.ROUVINEN,J.JANIS,R.K.WIERENGA JRNL TITL THE PEROXISOMAL ZEBRAFISH SCP2-THIOLASE (TYPE-1) IS A WEAK JRNL TITL 2 TRANSIENT DIMER AS REVEALED BY CRYSTAL STRUCTURES AND NATIVE JRNL TITL 3 MASS SPECTROMETRY. JRNL REF BIOCHEM. J. V. 476 307 2019 JRNL REFN ESSN 1470-8728 JRNL PMID 30573650 JRNL DOI 10.1042/BCJ20180788 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 57744 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3040 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) : 4266 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 225 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19000 REMARK 3 B22 (A**2) : 0.22000 REMARK 3 B33 (A**2) : -0.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.97000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.693 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5980 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5503 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8069 ; 1.498 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12793 ; 0.950 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 767 ; 6.088 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;36.815 ;24.618 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1009 ;13.749 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;12.675 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 877 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6749 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1178 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; 0.154 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5862 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 5730 ; 0.076 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 558 ; 0.128 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.048 ; 0.200 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): 28 ; 0.106 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 115 ; 0.150 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.166 ; 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): 3084 ; 2.031 ; 3.251 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3082 ; 2.032 ; 3.250 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3845 ; 2.801 ; 4.859 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3846 ; 2.800 ; 4.860 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2896 ; 2.822 ; 3.620 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2897 ; 2.822 ; 3.621 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4224 ; 4.301 ; 5.277 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4225 ; 4.300 ; 5.277 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6588 ; 5.212 ;38.692 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6589 ; 5.212 ;38.695 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 : NULL 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 6HRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200012131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JULY 4, 2012 REMARK 200 DATA SCALING SOFTWARE : XSCALE NOVEMBER 3, 2014 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60799 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 29.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42000 REMARK 200 FOR SHELL : 2.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.1 REMARK 200 STARTING MODEL: 3ZBG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 6.4, 18% PEG3350, 250 REMARK 280 MM SODIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.58000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.58000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.97000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 76.51654 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.50920 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 617 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 704 LIES ON A SPECIAL POSITION. 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 -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 90 REMARK 465 ARG A 119 REMARK 465 GLY A 120 REMARK 465 SER A 121 REMARK 465 LEU A 122 REMARK 465 SER A 123 REMARK 465 SER A 124 REMARK 465 LYS A 125 REMARK 465 TYR A 126 REMARK 465 MET A 127 REMARK 465 ASP A 128 REMARK 465 ARG A 129 REMARK 465 THR A 130 REMARK 465 ASN A 131 REMARK 465 GLN A 402 REMARK 465 GLU A 403 REMARK 465 THR A 404 REMARK 465 SER A 405 REMARK 465 SER A 406 REMARK 465 ARG A 407 REMARK 465 ILE A 408 REMARK 465 ALA A 409 REMARK 465 ALA A 410 REMARK 465 VAL A 411 REMARK 465 SER A 412 REMARK 465 THR A 413 REMARK 465 MET B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 LEU B 4 REMARK 465 ARG B 5 REMARK 465 ARG B 119 REMARK 465 GLY B 120 REMARK 465 SER B 121 REMARK 465 LEU B 122 REMARK 465 SER B 123 REMARK 465 SER B 124 REMARK 465 GLN B 402 REMARK 465 GLU B 403 REMARK 465 THR B 404 REMARK 465 SER B 405 REMARK 465 SER B 406 REMARK 465 ARG B 407 REMARK 465 ILE B 408 REMARK 465 ALA B 409 REMARK 465 ALA B 410 REMARK 465 VAL B 411 REMARK 465 SER B 412 REMARK 465 THR B 413 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 SER A 88 -40.64 -133.87 REMARK 500 GLU A 210 -141.24 61.67 REMARK 500 SER B 72 -64.04 -120.20 REMARK 500 ASN B 85 47.82 -167.52 REMARK 500 ASN B 86 -124.52 49.46 REMARK 500 PHE B 209 116.13 -160.62 REMARK 500 GLU B 210 -132.61 55.07 REMARK 500 ASP B 299 55.85 -96.33 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 GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 502 DBREF 6HRV A 1 413 UNP Q6P4V5 Q6P4V5_DANRE 1 413 DBREF 6HRV B 1 413 UNP Q6P4V5 Q6P4V5_DANRE 1 413 SEQADV 6HRV MET A -7 UNP Q6P4V5 INITIATING METHIONINE SEQADV 6HRV HIS A -6 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS A -5 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS A -4 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS A -3 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS A -2 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS A -1 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV ALA A 0 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV MET B -7 UNP Q6P4V5 INITIATING METHIONINE SEQADV 6HRV HIS B -6 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS B -5 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS B -4 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS B -3 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS B -2 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV HIS B -1 UNP Q6P4V5 EXPRESSION TAG SEQADV 6HRV ALA B 0 UNP Q6P4V5 EXPRESSION TAG SEQRES 1 A 421 MET HIS HIS HIS HIS HIS HIS ALA MET ALA ALA LEU ARG SEQRES 2 A 421 ASN ARG VAL PHE VAL ILE GLY VAL GLY MET THR LYS PHE SEQRES 3 A 421 GLU LYS PRO GLY ALA ARG ASP ILE ASP TYR PRO ASP MET SEQRES 4 A 421 ALA LYS GLU ALA GLY GLN ARG ALA LEU ALA ASP ALA GLY SEQRES 5 A 421 ILE LYS TYR SER ALA ILE GLN GLN ALA CYS VAL GLY TYR SEQRES 6 A 421 VAL TYR GLY ASP SER THR CYS GLY GLN ARG ALA ILE TYR SEQRES 7 A 421 HIS SER LEU GLY LEU SER GLY ILE PRO ILE ILE ASN VAL SEQRES 8 A 421 ASN ASN ASN CYS SER THR GLY SER THR ALA LEU PHE MET SEQRES 9 A 421 GLY ARG GLN LEU ILE GLN GLY GLY LEU ALA ASP CYS VAL SEQRES 10 A 421 LEU ALA LEU GLY PHE GLU LYS MET GLU ARG GLY SER LEU SEQRES 11 A 421 SER SER LYS TYR MET ASP ARG THR ASN PRO MET ASP LYS SEQRES 12 A 421 HIS MET GLU VAL MET ILE ASN ARG TYR GLY LEU ALA ALA SEQRES 13 A 421 VAL PRO ALA ALA PRO GLN MET PHE GLY ASN ALA GLY ARG SEQRES 14 A 421 GLU HIS MET GLU LYS TYR GLY THR LYS PRO GLU HIS PHE SEQRES 15 A 421 ALA LYS VAL ALA TRP LYS ASN HIS LYS HIS SER THR ASN SEQRES 16 A 421 ASN PRO TYR SER GLN PHE GLN ASP GLU TYR SER LEU GLU SEQRES 17 A 421 GLN VAL ILE ASP SER ARG LYS VAL PHE GLU PHE LEU THR SEQRES 18 A 421 LEU LEU GLN CYS CYS PRO THR SER ASP GLY ALA GLY ALA SEQRES 19 A 421 ALA VAL LEU ALA SER GLU SER PHE VAL ARG ARG ASN GLY SEQRES 20 A 421 LEU GLU LYS LYS ALA VAL GLU ILE VAL ALA GLN GLU MET SEQRES 21 A 421 VAL THR ASP LEU SER THR THR PHE GLU GLU ASN SER CYS SEQRES 22 A 421 MET LYS MET VAL GLY TYR ASP MET THR ARG LEU ALA ALA SEQRES 23 A 421 GLU ARG CYS TYR ASP THR ALA GLY VAL LYS PRO SER ASP SEQRES 24 A 421 VAL ASP VAL ILE GLU LEU HIS ASP CYS PHE SER ALA ASN SEQRES 25 A 421 GLU LEU ILE THR TYR GLU ALA LEU GLY LEU CYS PRO GLU SEQRES 26 A 421 GLY LYS ALA GLY GLU LEU ILE ASP ARG GLY ASP ASN THR SEQRES 27 A 421 TYR GLY GLY LYS TRP VAL ILE ASN PRO SER GLY GLY LEU SEQRES 28 A 421 ILE SER LYS GLY HIS PRO LEU GLY ALA THR GLY LEU ALA SEQRES 29 A 421 GLN CYS ALA GLU LEU CYS TRP GLN LEU ARG ALA GLU ALA SEQRES 30 A 421 GLY PRO ARG GLN VAL PRO GLY ALA LYS LEU ALA LEU GLN SEQRES 31 A 421 HIS ASN ILE GLY LEU GLY GLY ALA VAL VAL VAL THR LEU SEQRES 32 A 421 TYR LYS MET GLY PHE PRO GLN GLU THR SER SER ARG ILE SEQRES 33 A 421 ALA ALA VAL SER THR SEQRES 1 B 421 MET HIS HIS HIS HIS HIS HIS ALA MET ALA ALA LEU ARG SEQRES 2 B 421 ASN ARG VAL PHE VAL ILE GLY VAL GLY MET THR LYS PHE SEQRES 3 B 421 GLU LYS PRO GLY ALA ARG ASP ILE ASP TYR PRO ASP MET SEQRES 4 B 421 ALA LYS GLU ALA GLY GLN ARG ALA LEU ALA ASP ALA GLY SEQRES 5 B 421 ILE LYS TYR SER ALA ILE GLN GLN ALA CYS VAL GLY TYR SEQRES 6 B 421 VAL TYR GLY ASP SER THR CYS GLY GLN ARG ALA ILE TYR SEQRES 7 B 421 HIS SER LEU GLY LEU SER GLY ILE PRO ILE ILE ASN VAL SEQRES 8 B 421 ASN ASN ASN CSO SER THR GLY SER THR ALA LEU PHE MET SEQRES 9 B 421 GLY ARG GLN LEU ILE GLN GLY GLY LEU ALA ASP CYS VAL SEQRES 10 B 421 LEU ALA LEU GLY PHE GLU LYS MET GLU ARG GLY SER LEU SEQRES 11 B 421 SER SER LYS TYR MET ASP ARG THR ASN PRO MET ASP LYS SEQRES 12 B 421 HIS MET GLU VAL MET ILE ASN ARG TYR GLY LEU ALA ALA SEQRES 13 B 421 VAL PRO ALA ALA PRO GLN MET PHE GLY ASN ALA GLY ARG SEQRES 14 B 421 GLU HIS MET GLU LYS TYR GLY THR LYS PRO GLU HIS PHE SEQRES 15 B 421 ALA LYS VAL ALA TRP LYS ASN HIS LYS HIS SER THR ASN SEQRES 16 B 421 ASN PRO TYR SER GLN PHE GLN ASP GLU TYR SER LEU GLU SEQRES 17 B 421 GLN VAL ILE ASP SER ARG LYS VAL PHE GLU PHE LEU THR SEQRES 18 B 421 LEU LEU GLN CYS CYS PRO THR SER ASP GLY ALA GLY ALA SEQRES 19 B 421 ALA VAL LEU ALA SER GLU SER PHE VAL ARG ARG ASN GLY SEQRES 20 B 421 LEU GLU LYS LYS ALA VAL GLU ILE VAL ALA GLN GLU MET SEQRES 21 B 421 VAL THR ASP LEU SER THR THR PHE GLU GLU ASN SER CYS SEQRES 22 B 421 MET LYS MET VAL GLY TYR ASP MET THR ARG LEU ALA ALA SEQRES 23 B 421 GLU ARG CYS TYR ASP THR ALA GLY VAL LYS PRO SER ASP SEQRES 24 B 421 VAL ASP VAL ILE GLU LEU HIS ASP CYS PHE SER ALA ASN SEQRES 25 B 421 GLU LEU ILE THR TYR GLU ALA LEU GLY LEU CYS PRO GLU SEQRES 26 B 421 GLY LYS ALA GLY GLU LEU ILE ASP ARG GLY ASP ASN THR SEQRES 27 B 421 TYR GLY GLY LYS TRP VAL ILE ASN PRO SER GLY GLY LEU SEQRES 28 B 421 ILE SER LYS GLY HIS PRO LEU GLY ALA THR GLY LEU ALA SEQRES 29 B 421 GLN CYS ALA GLU LEU CYS TRP GLN LEU ARG ALA GLU ALA SEQRES 30 B 421 GLY PRO ARG GLN VAL PRO GLY ALA LYS LEU ALA LEU GLN SEQRES 31 B 421 HIS ASN ILE GLY LEU GLY GLY ALA VAL VAL VAL THR LEU SEQRES 32 B 421 TYR LYS MET GLY PHE PRO GLN GLU THR SER SER ARG ILE SEQRES 33 B 421 ALA ALA VAL SER THR MODRES 6HRV CSO B 87 CYS MODIFIED RESIDUE HET CSO B 87 7 HET GOL A 501 6 HET ACT A 502 4 HETNAM CSO S-HYDROXYCYSTEINE HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CSO C3 H7 N O3 S FORMUL 3 GOL C3 H8 O3 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 HOH *242(H2 O) HELIX 1 AA1 ASP A 27 GLY A 44 1 18 HELIX 2 AA2 LYS A 46 ILE A 50 5 5 HELIX 3 AA3 THR A 63 GLY A 74 1 12 HELIX 4 AA4 THR A 92 GLY A 103 1 12 HELIX 5 AA5 MET A 133 GLY A 145 1 13 HELIX 6 AA6 ALA A 151 GLY A 168 1 18 HELIX 7 AA7 LYS A 170 THR A 186 1 17 HELIX 8 AA8 SER A 198 SER A 205 1 8 HELIX 9 AA9 LEU A 215 CYS A 217 5 3 HELIX 10 AB1 GLU A 232 ASN A 238 1 7 HELIX 11 AB2 SER A 264 VAL A 269 1 6 HELIX 12 AB3 GLY A 270 GLY A 286 1 17 HELIX 13 AB4 LYS A 288 VAL A 292 5 5 HELIX 14 AB5 PHE A 301 LEU A 312 1 12 HELIX 15 AB6 LYS A 319 ARG A 326 1 8 HELIX 16 AB7 GLY A 341 GLY A 347 1 7 HELIX 17 AB8 ALA A 352 ARG A 366 1 15 HELIX 18 AB9 ALA A 369 GLN A 373 5 5 HELIX 19 AC1 ASP B 27 GLY B 44 1 18 HELIX 20 AC2 LYS B 46 ILE B 50 5 5 HELIX 21 AC3 THR B 63 TYR B 70 1 8 HELIX 22 AC4 ASN B 85 CSO B 87 5 3 HELIX 23 AC5 SER B 88 GLY B 103 1 16 HELIX 24 AC6 MET B 133 GLY B 145 1 13 HELIX 25 AC7 PRO B 150 GLY B 168 1 19 HELIX 26 AC8 LYS B 170 THR B 186 1 17 HELIX 27 AC9 SER B 198 SER B 205 1 8 HELIX 28 AD1 LEU B 215 CYS B 217 5 3 HELIX 29 AD2 GLU B 232 ASN B 238 1 7 HELIX 30 AD3 LEU B 240 LYS B 243 5 4 HELIX 31 AD4 SER B 257 GLU B 262 1 6 HELIX 32 AD5 SER B 264 VAL B 269 1 6 HELIX 33 AD6 GLY B 270 GLY B 286 1 17 HELIX 34 AD7 LYS B 288 VAL B 292 5 5 HELIX 35 AD8 PHE B 301 LEU B 312 1 12 HELIX 36 AD9 LYS B 319 ARG B 326 1 8 HELIX 37 AE1 GLY B 341 GLY B 347 1 7 HELIX 38 AE2 ALA B 352 ARG B 366 1 15 HELIX 39 AE3 ALA B 369 GLN B 373 5 5 SHEET 1 AA110 ILE A 80 ASN A 82 0 SHEET 2 AA110 GLN A 52 GLY A 56 1 N ALA A 53 O ILE A 81 SHEET 3 AA110 CYS A 108 GLU A 115 1 O LEU A 112 N GLY A 56 SHEET 4 AA110 GLY A 223 SER A 231 -1 O ALA A 227 N ALA A 111 SHEET 5 AA110 VAL A 8 MET A 15 -1 N PHE A 9 O ALA A 230 SHEET 6 AA110 VAL A 245 VAL A 253 -1 O VAL A 245 N VAL A 10 SHEET 7 AA110 VAL A 391 MET A 398 -1 O VAL A 393 N GLU A 251 SHEET 8 AA110 ALA A 380 ILE A 385 -1 N ASN A 384 O VAL A 392 SHEET 9 AA110 VAL A 294 GLU A 296 1 N GLU A 296 O LEU A 381 SHEET 10 AA110 VAL A 336 ILE A 337 1 O VAL A 336 N ILE A 295 SHEET 1 AA2 2 LYS A 207 PHE A 209 0 SHEET 2 AA2 2 LEU A 212 THR A 213 -1 O LEU A 212 N VAL A 208 SHEET 1 AA310 ILE B 80 VAL B 83 0 SHEET 2 AA310 ALA B 53 GLY B 56 1 N VAL B 55 O ILE B 81 SHEET 3 AA310 CYS B 108 GLU B 115 1 O LEU B 112 N GLY B 56 SHEET 4 AA310 GLY B 223 SER B 231 -1 O ALA B 227 N ALA B 111 SHEET 5 AA310 VAL B 8 MET B 15 -1 N PHE B 9 O ALA B 230 SHEET 6 AA310 VAL B 245 VAL B 253 -1 O VAL B 245 N VAL B 10 SHEET 7 AA310 ALA B 390 MET B 398 -1 O LEU B 395 N ALA B 249 SHEET 8 AA310 ALA B 380 GLY B 386 -1 N GLN B 382 O THR B 394 SHEET 9 AA310 VAL B 294 GLU B 296 1 N GLU B 296 O HIS B 383 SHEET 10 AA310 VAL B 336 ILE B 337 1 O VAL B 336 N ILE B 295 SHEET 1 AA4 2 LYS B 207 PHE B 209 0 SHEET 2 AA4 2 LEU B 212 THR B 213 -1 O LEU B 212 N VAL B 208 LINK C ASN B 86 N CSO B 87 1555 1555 1.34 LINK C CSO B 87 N SER B 88 1555 1555 1.34 CISPEP 1 GLY B 388 GLY B 389 0 1.55 SITE 1 AC1 4 TYR A 59 GLU A 115 LYS A 116 GLU A 118 SITE 1 AC2 9 THR A 92 LEU A 94 GLN A 250 GLN A 382 SITE 2 AC2 9 ASN A 384 VAL A 392 THR A 394 HOH A 653 SITE 3 AC2 9 HOH A 716 CRYST1 133.160 81.940 96.810 90.00 125.81 90.00 C 1 2 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 0.007510 0.000000 0.005418 0.00000 SCALE2 0.000000 0.012204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012737 0.00000