HEADER ISOMERASE, CHAPERONE 10-JAN-14 4ODK TITLE STRUCTURE OF SLYD FROM THERMUS THERMOPHILUS IN COMPLEX WITH T1 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TTSLYD; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GUANYL-SPECIFIC RIBONUCLEASE T1; COMPND 9 CHAIN: B, C; COMPND 10 FRAGMENT: T1 PEPTIDE (UNP RESIDUES 59-73); COMPND 11 SYNONYM: RNASE T1; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: TTHA0346; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ASPERGILLUS ORYZAE; SOURCE 10 ORGANISM_COMMON: YELLOW KOJI MOLD; SOURCE 11 ORGANISM_TAXID: 5062 KEYWDS FKBP DOMAIN, IF DOMAIN, CHAPERONE, PEPTIDYL-PROLYL ISOMERASE, PPIASE, KEYWDS 2 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.M.QUISTGAARD,C.LOW,P.NORDLUND REVDAT 2 04-OCT-17 4ODK 1 JRNL REVDAT 1 14-JAN-15 4ODK 0 JRNL AUTH E.M.QUISTGAARD,U.WEININGER,Y.URAL-BLIMKE,K.MODIG,P.NORDLUND, JRNL AUTH 2 M.AKKE,C.LOW JRNL TITL MOLECULAR INSIGHTS INTO SUBSTRATE RECOGNITION AND CATALYTIC JRNL TITL 2 MECHANISM OF THE CHAPERONE AND FKBP PEPTIDYL-PROLYL JRNL TITL 3 ISOMERASE SLYD. JRNL REF BMC BIOL. V. 14 82 2016 JRNL REFN ESSN 1741-7007 JRNL PMID 27664121 JRNL DOI 10.1186/S12915-016-0300-3 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 40188 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.1019 - 2.9124 0.98 4392 169 0.1520 0.1748 REMARK 3 2 2.9124 - 2.3119 0.99 4386 142 0.1584 0.1664 REMARK 3 3 2.3119 - 2.0198 0.99 4365 145 0.1124 0.1483 REMARK 3 4 2.0198 - 1.8351 0.98 4331 156 0.0948 0.1431 REMARK 3 5 1.8351 - 1.7036 0.98 4315 163 0.0952 0.1371 REMARK 3 6 1.7036 - 1.6032 0.98 4324 115 0.0978 0.1469 REMARK 3 7 1.6032 - 1.5229 0.98 4350 127 0.1203 0.1872 REMARK 3 8 1.5229 - 1.4566 0.97 4305 114 0.1585 0.2030 REMARK 3 9 1.4566 - 1.4010 0.95 4165 124 0.2206 0.2833 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1376 REMARK 3 ANGLE : 1.027 1888 REMARK 3 CHIRALITY : 0.071 202 REMARK 3 PLANARITY : 0.006 258 REMARK 3 DIHEDRAL : 12.692 517 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PDB ENTRY 3LUO REMARK 4 REMARK 4 4ODK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9191 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40188 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02300 REMARK 200 FOR THE DATA SET : 23.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.71400 REMARK 200 FOR SHELL : 2.020 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13.2% PEG1500, 0.1 M HEPES, PH 7.5, REMARK 280 0.05 M SODIUM CHLORIDE, 11% GLYCEROL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 43.75000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.75000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.49500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 96 REMARK 465 GLU A 97 REMARK 465 GLY A 98 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 465 VAL B 59 REMARK 465 GLY B 60 REMARK 465 SER B 61 REMARK 465 ASN B 62 REMARK 465 SER B 63 REMARK 465 TYR B 64 REMARK 465 PRO B 65 REMARK 465 VAL C 59 REMARK 465 GLY C 60 REMARK 465 SER C 61 REMARK 465 ASN C 62 REMARK 465 SER C 63 REMARK 465 LYS C 67 REMARK 465 TYR C 68 REMARK 465 ASN C 69 REMARK 465 ASN C 70 REMARK 465 TYR C 71 REMARK 465 GLU C 72 REMARK 465 GLY C 73 REMARK 465 NH2 C 74 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 HOH A 313 O HOH A 468 2.14 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 ALA A 62 -107.24 -116.24 REMARK 500 SER A 151 23.53 -140.01 REMARK 500 PRO C 65 38.72 -99.70 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 CL A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ODL RELATED DB: PDB REMARK 900 RELATED ID: 4ODM RELATED DB: PDB REMARK 900 RELATED ID: 4ODN RELATED DB: PDB REMARK 900 RELATED ID: 4ODO RELATED DB: PDB REMARK 900 RELATED ID: 4ODP RELATED DB: PDB REMARK 900 RELATED ID: 4ODQ RELATED DB: PDB REMARK 900 RELATED ID: 4ODR RELATED DB: PDB DBREF 4ODK A 1 149 UNP Q5SLE7 Q5SLE7_THET8 1 149 DBREF 4ODK B 59 73 UNP P00651 RNT1_ASPOR 59 73 DBREF 4ODK C 59 73 UNP P00651 RNT1_ASPOR 59 73 SEQADV 4ODK PRO A 150 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK SER A 151 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK GLY A 152 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK HIS A 153 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK HIS A 154 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK HIS A 155 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK HIS A 156 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK HIS A 157 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK HIS A 158 UNP Q5SLE7 EXPRESSION TAG SEQADV 4ODK NH2 B 74 UNP P00651 AMIDATION SEQADV 4ODK NH2 C 74 UNP P00651 AMIDATION SEQRES 1 A 158 MET LYS VAL GLY GLN ASP LYS VAL VAL THR ILE ARG TYR SEQRES 2 A 158 THR LEU GLN VAL GLU GLY GLU VAL LEU ASP GLN GLY GLU SEQRES 3 A 158 LEU SER TYR LEU HIS GLY HIS ARG ASN LEU ILE PRO GLY SEQRES 4 A 158 LEU GLU GLU ALA LEU GLU GLY ARG GLU GLU GLY GLU ALA SEQRES 5 A 158 PHE GLN ALA HIS VAL PRO ALA GLU LYS ALA TYR GLY PRO SEQRES 6 A 158 HIS ASP PRO GLU GLY VAL GLN VAL VAL PRO LEU SER ALA SEQRES 7 A 158 PHE PRO GLU ASP ALA GLU VAL VAL PRO GLY ALA GLN PHE SEQRES 8 A 158 TYR ALA GLN ASP MET GLU GLY ASN PRO MET PRO LEU THR SEQRES 9 A 158 VAL VAL ALA VAL GLU GLY GLU GLU VAL THR VAL ASP PHE SEQRES 10 A 158 ASN HIS PRO LEU ALA GLY LYS ASP LEU ASP PHE GLN VAL SEQRES 11 A 158 GLU VAL VAL LYS VAL ARG GLU ALA THR PRO GLU GLU LEU SEQRES 12 A 158 LEU HIS GLY HIS ALA HIS PRO SER GLY HIS HIS HIS HIS SEQRES 13 A 158 HIS HIS SEQRES 1 B 16 VAL GLY SER ASN SER TYR PRO HIS LYS TYR ASN ASN TYR SEQRES 2 B 16 GLU GLY NH2 SEQRES 1 C 16 VAL GLY SER ASN SER TYR PRO HIS LYS TYR ASN ASN TYR SEQRES 2 C 16 GLU GLY NH2 HET NH2 B 74 1 HET CL A 201 1 HETNAM NH2 AMINO GROUP HETNAM CL CHLORIDE ION FORMUL 2 NH2 H2 N FORMUL 4 CL CL 1- FORMUL 5 HOH *195(H2 O) HELIX 1 1 ILE A 37 GLU A 45 1 9 HELIX 2 2 PRO A 58 ALA A 62 5 5 HELIX 3 3 ASP A 67 GLU A 69 5 3 HELIX 4 4 SER A 77 PHE A 79 5 3 HELIX 5 5 THR A 139 GLY A 146 1 8 SHEET 1 A 5 ALA A 52 VAL A 57 0 SHEET 2 A 5 LEU A 126 GLU A 137 -1 O LEU A 126 N VAL A 57 SHEET 3 A 5 LYS A 7 VAL A 17 -1 N VAL A 8 O ARG A 136 SHEET 4 A 5 GLU A 20 LEU A 30 -1 O ASP A 23 N LEU A 15 SHEET 5 A 5 HIS A 154 HIS A 156 -1 O HIS A 156 N GLN A 24 SHEET 1 B 4 VAL A 71 PRO A 75 0 SHEET 2 B 4 GLU A 112 ASP A 116 -1 O VAL A 115 N GLN A 72 SHEET 3 B 4 MET A 101 GLU A 109 -1 N GLU A 109 O GLU A 112 SHEET 4 B 4 GLN A 90 ALA A 93 -1 N ALA A 93 O MET A 101 LINK C GLY B 73 N NH2 B 74 1555 1555 1.33 CISPEP 1 TYR C 64 PRO C 65 0 -6.33 SITE 1 AC1 6 TYR A 29 LEU A 30 ASN A 35 HIS A 147 SITE 2 AC1 6 ALA A 148 HOH C 101 CRYST1 87.500 52.990 48.910 90.00 111.18 90.00 C 1 2 1 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 0.011429 0.000000 0.004427 0.00000 SCALE2 0.000000 0.018871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021926 0.00000