10 20 30 40 50 60 70 80 1URM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIOXIDANT ENZYME 31-OCT-03 1URM
TITLE HUMAN PEROXIREDOXIN 5, C47S MUTANT
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIREDOXIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 54-214; COMPND 5 SYNONYM: PRX-V, PEROXISOMAL ANTIOXIDANT ENZYME, PLP, THIOREDOXIN COMPND 6 PEROXIDASE PMP20, ANTIOXIDANT ENZYME B166, AOEB166, TPX TYPE VI, COMPND 7 ALU CO-REPRESSOR 1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: MUTATION CYS 47 SER IN COORDINATES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: LUNG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE-30
KEYWDS ANTIOXIDANT ENZYME, PEROXIREDOXIN, THIOREDOXIN PEROXIDASE, KEYWDS 2 THIOREDOXIN FOLD
EXPDTA X-RAY DIFFRACTION
AUTHOR J.P.DECLERCQ,C.EVRARD
REVDAT 3 13-JUL-11 1URM 1 VERSN REVDAT 2 24-FEB-09 1URM 1 VERSN REVDAT 1 29-SEP-04 1URM 0
JRNL AUTH C.EVRARD,A.SMEETS,B.KNOOPS,J.P.DECLERCQ JRNL TITL CRYSTAL STRUCTURE OF THE C47S MUTANT OF HUMAN PEROXIREDOXIN JRNL TITL 2 5 JRNL REF J. CHEM. CRYST. V. 34 553 2004 JRNL REFN ISSN 1074-1542 JRNL DOI 10.1023/B:JOCC.0000042025.08082.6C
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.P.DECLERCQ,C.EVRARD,A.CLIPPE,D.VANDERSTRICHT,A.BERNARD, REMARK 1 AUTH 2 B.KNOOPS REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN PEROXIREDOXIN 5, A NOVEL TYPE OF REMARK 1 TITL 2 MAMMALIAN PEROXIREDOXIN AT 1.5 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 311 751 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11518528 REMARK 1 DOI 10.1006/JMBI.2001.4853 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.P.DECLERCQ,C.EVRARD REMARK 1 TITL A TWINNED MONOCLINIC CRYSTAL FORM OF HUMAN PEROXIREDOXIN 5 REMARK 1 TITL 2 WITH EIGHT MOLECULES IN THE ASYMMETRIC UNIT REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 1829 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11717495 REMARK 1 DOI 10.1107/S0907444901015475 REMARK 1 REFERENCE 3 REMARK 1 AUTH B.KNOOPS,A.CLIPPE,C.BOGARD,K.ARSALANE,R.WATTIEZ,C.HERMANS, REMARK 1 AUTH 2 E.DUCONSEILLE,P.FALMAGNE,A.BERNARD REMARK 1 TITL CLONING AND CHARACTERIZATION OF AOEB166, A NOVEL MAMMALIAN REMARK 1 TITL 2 ANTIOXIDANT ENZYME OF THE PEROXIREDOXIN FAMILY REMARK 1 REF J.BIOL.CHEM. V. 274 30451 1999 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10521424 REMARK 1 DOI 10.1074/JBC.274.43.30451
REMARK 2 REMARK 2 RESOLUTION. 1.7 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28558 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1527 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2072 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.1710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1248 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 285 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) : 15.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.93000 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): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.189 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1278 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1194 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1729 ; 1.630 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2808 ; 0.842 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 161 ; 5.913 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 202 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1409 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 226 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 330 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1668 ; 0.260 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 921 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 235 ; 0.157 ; 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): 14 ; 0.143 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.213 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.157 ; 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): 814 ; 0.822 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1316 ; 1.490 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 464 ; 2.437 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 413 ; 4.045 ; 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 : 1 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 161 REMARK 3 ORIGIN FOR THE GROUP (A): 7.7770 41.8070 20.1220 REMARK 3 T TENSOR REMARK 3 T11: 0.0294 T22: 0.0316 REMARK 3 T33: 0.0130 T12: -0.0060 REMARK 3 T13: -0.0071 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.7648 L22: 1.3727 REMARK 3 L33: 1.4383 L12: 0.0261 REMARK 3 L13: 0.0285 L23: 0.6693 REMARK 3 S TENSOR REMARK 3 S11: -0.0464 S12: 0.0983 S13: -0.0215 REMARK 3 S21: -0.1138 S22: -0.0462 S23: 0.0957 REMARK 3 S31: 0.0458 S32: -0.1566 S33: 0.0926 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 1URM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-03. REMARK 100 THE PDBE ID CODE IS EBI-13842.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9911 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL FOCUSING REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.29200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1HD2 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.5 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.4 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED REMARK 280 FROM 1.6 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE REMARK 280 BUFFER PH 5.3, 0.2 M POTASSIUM SODIUM TARTRATE, REMARK 280 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE
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 61.02150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.82300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.82300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.51075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.82300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.82300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.53225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.82300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.82300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.51075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.82300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.82300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 91.53225 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 61.02150 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: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A2073 LIES ON A SPECIAL POSITION.
REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED MUTATION CYS 100 SER (FOLLOWING NUMBERING REMARK 400 OF THE SWISSPROT DATABASE REFERENCE). REMARK 400 REMARK 400 FUNCTION REMARK 400 REDUCES HYDROGEN PEROXIDE AND HYDROPEROXIDES WITH REMARK 400 REDUCING EQUIVALENTS USING THE THIOREDOXIN SYSTEM.
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 ARG A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 HIS 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 GLY A -1
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 50 -56.93 -122.78 REMARK 500 LYS A 93 -52.14 -120.91 REMARK 500 ASP A 113 -152.80 -88.60 REMARK 500 THR A 150 -99.75 -136.02 REMARK 500 REMARK 500 REMARK: NULL
REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEZ A 201
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H4O RELATED DB: PDB REMARK 900 MONOCLINIC FORM OF HUMAN PEROXIREDOXIN 5 REMARK 900 RELATED ID: 1HD2 RELATED DB: PDB REMARK 900 HUMAN PEROXIREDOXIN 5 REMARK 900 RELATED ID: 1OC3 RELATED DB: PDB REMARK 900 HUMAN PEROXIREDOXIN 5
REMARK 999 REMARK 999 SEQUENCE REMARK 999 C47S MUTANT
DBREF 1URM A -10 0 PDB 1URM 1URM -10 0 DBREF 1URM A 1 161 UNP P30044 PDX5_HUMAN 54 214
SEQADV 1URM SER A 47 UNP P30044 CYS 100 ENGINEERED MUTATION
SEQRES 1 A 172 ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ALA PRO SEQRES 2 A 172 ILE LYS VAL GLY ASP ALA ILE PRO ALA VAL GLU VAL PHE SEQRES 3 A 172 GLU GLY GLU PRO GLY ASN LYS VAL ASN LEU ALA GLU LEU SEQRES 4 A 172 PHE LYS GLY LYS LYS GLY VAL LEU PHE GLY VAL PRO GLY SEQRES 5 A 172 ALA PHE THR PRO GLY SER SER LYS THR HIS LEU PRO GLY SEQRES 6 A 172 PHE VAL GLU GLN ALA GLU ALA LEU LYS ALA LYS GLY VAL SEQRES 7 A 172 GLN VAL VAL ALA CYS LEU SER VAL ASN ASP ALA PHE VAL SEQRES 8 A 172 THR GLY GLU TRP GLY ARG ALA HIS LYS ALA GLU GLY LYS SEQRES 9 A 172 VAL ARG LEU LEU ALA ASP PRO THR GLY ALA PHE GLY LYS SEQRES 10 A 172 GLU THR ASP LEU LEU LEU ASP ASP SER LEU VAL SER ILE SEQRES 11 A 172 PHE GLY ASN ARG ARG LEU LYS ARG PHE SER MET VAL VAL SEQRES 12 A 172 GLN ASP GLY ILE VAL LYS ALA LEU ASN VAL GLU PRO ASP SEQRES 13 A 172 GLY THR GLY LEU THR CYS SER LEU ALA PRO ASN ILE ILE SEQRES 14 A 172 SER GLN LEU
HET CL A1162 1 HET CL A1163 1 HET CL A1164 1 HET BEZ A 201 9
HETNAM CL CHLORIDE ION HETNAM BEZ BENZOIC ACID
FORMUL 2 CL 3(CL 1-) FORMUL 5 BEZ C7 H6 O2 FORMUL 6 HOH *285(H2 O)
HELIX 1 1 LEU A 25 PHE A 29 1 5 HELIX 2 2 THR A 44 ALA A 64 1 21 HELIX 3 3 ASP A 77 HIS A 88 1 12 HELIX 4 4 GLY A 102 ASP A 109 1 8 HELIX 5 5 LEU A 116 GLY A 121 1 6 HELIX 6 6 LEU A 153 SER A 159 1 7
SHEET 1 AA 2 GLU A 13 PHE A 15 0 SHEET 2 AA 2 LYS A 22 ASN A 24 -1 O VAL A 23 N VAL A 14 SHEET 1 AB 5 ARG A 95 ALA A 98 0 SHEET 2 AB 5 VAL A 67 SER A 74 1 O VAL A 70 N ARG A 95 SHEET 3 AB 5 LYS A 33 GLY A 38 1 O LYS A 33 N GLN A 68 SHEET 4 AB 5 PHE A 128 GLN A 133 -1 O PHE A 128 N GLY A 38 SHEET 5 AB 5 ILE A 136 VAL A 142 -1 O ILE A 136 N GLN A 133
SITE 1 AC1 4 LYS A 63 LYS A 93 SER A 118 HOH A2189 SITE 1 AC2 4 ARG A 86 LYS A 89 ALA A 90 GLU A 91 SITE 1 AC3 5 GLY A 54 PRO A 155 HOH A2022 HOH A2123 SITE 2 AC3 5 HOH A2132 SITE 1 AC4 11 PRO A 40 THR A 44 PRO A 45 GLY A 46 SITE 2 AC4 11 SER A 47 LYS A 63 ALA A 64 PHE A 120 SITE 3 AC4 11 ARG A 127 THR A 147 HOH A2145
CRYST1 65.646 65.646 122.043 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 0.015233 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015233 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008194 0.00000