PDB Short entry for 2XRI HEADER HYDROLASE 15-SEP-10 2XRI TITLE CRYSTAL STRUCTURE OF HUMAN ERI1 EXORIBONUCLEASE 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERI1 EXORIBONUCLEASE 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 137-337; COMPND 5 SYNONYM: PRION PROTEIN-INTERACTING PROTEIN, PRION INTERACTOR 1; COMPND 6 EC: 3.1.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3 PRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4 KEYWDS HYDROLASE, METAL BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.WELIN,M.I.SIPONEN,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA,R.COLLINS, AUTHOR 2 A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,I.JOHANSSON, AUTHOR 3 T.KARLBERG,S.KOL,T.KOTENYOVA,E.KOUZNETSOVA,M.MOCHE,T.NYMAN, AUTHOR 4 C.PERSSON,H.SCHULER,P.SCHUTZ,A.G.THORSELL,L.TRESAUGUES,S.VAN DER AUTHOR 5 BERG,E.WAHLBERG,J.WEIGELT,P.NORDLUND REVDAT 4 20-DEC-23 2XRI 1 REMARK LINK REVDAT 3 27-NOV-13 2XRI 1 SOURCE REMARK VERSN HETSYN REVDAT 2 13-OCT-10 2XRI 1 AUTHOR REVDAT 1 29-SEP-10 2XRI 0 JRNL AUTH M.WELIN,M.I.SIPONEN,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA, JRNL AUTH 2 R.COLLINS,A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND, JRNL AUTH 3 M.HAMMARSTROM,I.JOHANSSON,T.KARLBERG,S.KOL,T.KOTENYOVA, JRNL AUTH 4 E.KOUZNETSOVA,M.MOCHE,T.NYMAN,C.PERSSON,H.SCHULER,P.SCHUTZ, JRNL AUTH 5 A.G.THORSELL,L.TRESAUGUES,S.VAN DER BERG,E.WAHLBERG, JRNL AUTH 6 J.WEIGELT,P.NORDLUND JRNL TITL CRYSTAL STRUCTURE OF HUMAN ERI1 EXORIBONUCLEASE 3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12235 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 644 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 875 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1665 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.01000 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): 0.225 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.175 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.134 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1716 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1180 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2322 ; 1.183 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2890 ; 0.858 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 6.743 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;36.278 ;24.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 300 ;12.230 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;17.910 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 248 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1863 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 334 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 301 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1147 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 806 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 819 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 95 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.051 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 36 ; 0.286 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.132 ; 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): 1340 ; 0.743 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 410 ; 0.125 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1671 ; 0.851 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 827 ; 1.609 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 651 ; 2.047 ; 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 : 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 130 A 336 REMARK 3 ORIGIN FOR THE GROUP (A): 13.9803 12.7294 -19.0152 REMARK 3 T TENSOR REMARK 3 T11: -0.0941 T22: -0.0859 REMARK 3 T33: -0.0636 T12: 0.0050 REMARK 3 T13: 0.0056 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 1.1828 L22: 1.3032 REMARK 3 L33: 3.2473 L12: -0.1519 REMARK 3 L13: -1.2247 L23: 0.2991 REMARK 3 S TENSOR REMARK 3 S11: -0.0732 S12: -0.0861 S13: -0.0818 REMARK 3 S21: -0.0400 S22: -0.0033 S23: -0.1825 REMARK 3 S31: 0.1775 S32: 0.1615 S33: 0.0765 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. REMARK 4 REMARK 4 2XRI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1290045387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-09 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97908 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12879 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 43.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1W0H REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.5 20% PEG MONOMETHYL REMARK 280 ETHER 2000 0.2M TRIMETHYLAMINE N-OXIDE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 34.36000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.49000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.49000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.45000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.49000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.45000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.49000 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 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 A2051 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 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 SER A 121 REMARK 465 SER A 122 REMARK 465 GLY A 123 REMARK 465 VAL A 124 REMARK 465 ASP A 125 REMARK 465 LEU A 126 REMARK 465 GLY A 127 REMARK 465 THR A 128 REMARK 465 GLU A 129 REMARK 465 PRO A 158 REMARK 465 PHE A 337 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 OE1 GLN A 214 O HOH A 2054 2.12 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 VAL A 252 -56.03 -125.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1337 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 150 OD2 REMARK 620 2 GLU A 152 OE2 111.8 REMARK 620 3 ASP A 312 OD2 98.1 122.9 REMARK 620 4 HOH A2020 O 112.6 95.0 117.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1338 DBREF 2XRI A 137 337 UNP O43414 ERI3_HUMAN 137 337 SEQADV 2XRI MET A 114 UNP O43414 EXPRESSION TAG SEQADV 2XRI HIS A 115 UNP O43414 EXPRESSION TAG SEQADV 2XRI HIS A 116 UNP O43414 EXPRESSION TAG SEQADV 2XRI HIS A 117 UNP O43414 EXPRESSION TAG SEQADV 2XRI HIS A 118 UNP O43414 EXPRESSION TAG SEQADV 2XRI HIS A 119 UNP O43414 EXPRESSION TAG SEQADV 2XRI HIS A 120 UNP O43414 EXPRESSION TAG SEQADV 2XRI SER A 121 UNP O43414 EXPRESSION TAG SEQADV 2XRI SER A 122 UNP O43414 EXPRESSION TAG SEQADV 2XRI GLY A 123 UNP O43414 EXPRESSION TAG SEQADV 2XRI VAL A 124 UNP O43414 EXPRESSION TAG SEQADV 2XRI ASP A 125 UNP O43414 EXPRESSION TAG SEQADV 2XRI LEU A 126 UNP O43414 EXPRESSION TAG SEQADV 2XRI GLY A 127 UNP O43414 EXPRESSION TAG SEQADV 2XRI THR A 128 UNP O43414 EXPRESSION TAG SEQADV 2XRI GLU A 129 UNP O43414 EXPRESSION TAG SEQADV 2XRI ASN A 130 UNP O43414 EXPRESSION TAG SEQADV 2XRI LEU A 131 UNP O43414 EXPRESSION TAG SEQADV 2XRI TYR A 132 UNP O43414 EXPRESSION TAG SEQADV 2XRI PHE A 133 UNP O43414 EXPRESSION TAG SEQADV 2XRI GLN A 134 UNP O43414 EXPRESSION TAG SEQADV 2XRI SER A 135 UNP O43414 EXPRESSION TAG SEQADV 2XRI MET A 136 UNP O43414 EXPRESSION TAG SEQRES 1 A 224 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 224 GLY THR GLU ASN LEU TYR PHE GLN SER MET SER PHE PRO SEQRES 3 A 224 PRO GLN ARG TYR HIS TYR PHE LEU VAL LEU ASP PHE GLU SEQRES 4 A 224 ALA THR CYS ASP LYS PRO GLN ILE HIS PRO GLN GLU ILE SEQRES 5 A 224 ILE GLU PHE PRO ILE LEU LYS LEU ASN GLY ARG THR MET SEQRES 6 A 224 GLU ILE GLU SER THR PHE HIS MET TYR VAL GLN PRO VAL SEQRES 7 A 224 VAL HIS PRO GLN LEU THR PRO PHE CYS THR GLU LEU THR SEQRES 8 A 224 GLY ILE ILE GLN ALA MET VAL ASP GLY GLN PRO SER LEU SEQRES 9 A 224 GLN GLN VAL LEU GLU ARG VAL ASP GLU TRP MET ALA LYS SEQRES 10 A 224 GLU GLY LEU LEU ASP PRO ASN VAL LYS SER ILE PHE VAL SEQRES 11 A 224 THR CYS GLY ASP TRP ASP LEU LYS VAL MET LEU PRO GLY SEQRES 12 A 224 GLN CYS GLN TYR LEU GLY LEU PRO VAL ALA ASP TYR PHE SEQRES 13 A 224 LYS GLN TRP ILE ASN LEU LYS LYS ALA TYR SER PHE ALA SEQRES 14 A 224 MET GLY CYS TRP PRO LYS ASN GLY LEU LEU ASP MET ASN SEQRES 15 A 224 LYS GLY LEU SER LEU GLN HIS ILE GLY ARG PRO HIS SER SEQRES 16 A 224 GLY ILE ASP ASP CYS LYS ASN ILE ALA ASN ILE MET LYS SEQRES 17 A 224 THR LEU ALA TYR ARG GLY PHE ILE PHE LYS GLN THR SER SEQRES 18 A 224 LYS PRO PHE HET MG A1337 1 HET GOL A1338 6 HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *104(H2 O) HELIX 1 1 ASN A 130 GLN A 134 5 5 HELIX 2 2 THR A 197 GLY A 205 1 9 HELIX 3 3 ILE A 207 ASP A 212 1 6 HELIX 4 4 SER A 216 GLU A 231 1 16 HELIX 5 5 ASP A 247 VAL A 252 1 6 HELIX 6 6 VAL A 252 GLY A 262 1 11 HELIX 7 7 ALA A 266 LYS A 270 5 5 HELIX 8 8 LEU A 275 GLY A 284 1 10 HELIX 9 9 GLY A 290 LEU A 298 1 9 HELIX 10 10 SER A 308 ARG A 326 1 19 SHEET 1 AA 2 GLU A 152 ALA A 153 0 SHEET 2 AA 2 ILE A 165 ASN A 174 -1 N ILE A 166 O GLU A 152 SHEET 1 AB 2 ILE A 180 TYR A 187 0 SHEET 2 AB 2 ILE A 165 ASN A 174 -1 O PHE A 168 N MET A 186 SHEET 1 AC 5 TRP A 272 ASN A 274 0 SHEET 2 AC 5 SER A 240 THR A 244 1 O PHE A 242 N ILE A 273 SHEET 3 AC 5 TYR A 145 LEU A 149 1 O TYR A 145 N ILE A 241 SHEET 4 AC 5 ILE A 165 ASN A 174 -1 O LEU A 171 N VAL A 148 SHEET 5 AC 5 ILE A 180 TYR A 187 -1 N GLU A 181 O LYS A 172 SHEET 1 AD 5 TRP A 272 ASN A 274 0 SHEET 2 AD 5 SER A 240 THR A 244 1 O PHE A 242 N ILE A 273 SHEET 3 AD 5 TYR A 145 LEU A 149 1 O TYR A 145 N ILE A 241 SHEET 4 AD 5 ILE A 165 ASN A 174 -1 O LEU A 171 N VAL A 148 SHEET 5 AD 5 GLU A 152 ALA A 153 -1 O GLU A 152 N ILE A 166 LINK OD2 ASP A 150 MG MG A1337 1555 1555 1.94 LINK OE2 GLU A 152 MG MG A1337 1555 1555 2.18 LINK OD2 ASP A 312 MG MG A1337 1555 1555 2.37 LINK MG MG A1337 O HOH A2020 1555 1555 2.53 CISPEP 1 HIS A 161 PRO A 162 0 -4.21 SITE 1 AC1 5 ASP A 150 PHE A 151 GLU A 152 ASP A 312 SITE 2 AC1 5 HOH A2020 SITE 1 AC2 5 GLU A 152 ALA A 153 CYS A 155 GLN A 163 SITE 2 AC2 5 LEU A 203 CRYST1 68.720 76.900 86.980 90.00 90.00 90.00 I 2 2 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 0.014552 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011497 0.00000