PDB Short entry for 2ZQT HEADER ISOMERASE 19-AUG-08 2ZQT TITLE CRYSTAL STRUCTURE OF A MUTANT PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, ROTAMASE PIN1, COMPND 5 PPIASE PIN1; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PIN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B+ KEYWDS PIN1 MUTANT M130A, CELL CYCLE, ISOMERASE, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 2 ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR C.JOBICHEN,Y.C.LIOU,J.SIVARAMAN REVDAT 3 01-NOV-23 2ZQT 1 REMARK REVDAT 2 10-NOV-21 2ZQT 1 REMARK SEQADV REVDAT 1 25-AUG-09 2ZQT 0 JRNL AUTH C.JOBICHEN,Y.C.LIOU,J.SIVARAMAN JRNL TITL STRUCTURAL STUDIES ON PIN1 MUTANTS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 28402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.190 REMARK 3 FREE R VALUE TEST SET COUNT : 3461 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 30.9575 - 4.2702 0.99 1196 166 0.2676 0.3298 REMARK 3 2 4.2702 - 3.3907 1.00 1095 166 0.2251 0.2393 REMARK 3 3 3.3907 - 2.9625 0.99 1095 132 0.2449 0.2837 REMARK 3 4 2.9625 - 2.6918 0.99 1045 172 0.2666 0.2949 REMARK 3 5 2.6918 - 2.4990 0.99 1059 141 0.2477 0.2714 REMARK 3 6 2.4990 - 2.3517 0.98 1054 137 0.2410 0.2427 REMARK 3 7 2.3517 - 2.2340 0.97 1006 151 0.2471 0.2448 REMARK 3 8 2.2340 - 2.1367 0.97 1056 139 0.2288 0.2280 REMARK 3 9 2.1367 - 2.0545 0.97 1025 133 0.2168 0.2645 REMARK 3 10 2.0545 - 1.9836 0.97 1041 119 0.2268 0.2346 REMARK 3 11 1.9836 - 1.9216 0.97 1005 152 0.2233 0.2842 REMARK 3 12 1.9216 - 1.8667 0.96 1005 150 0.2217 0.2232 REMARK 3 13 1.8667 - 1.8175 0.96 987 149 0.2124 0.2493 REMARK 3 14 1.8175 - 1.7732 0.95 985 150 0.2094 0.2718 REMARK 3 15 1.7732 - 1.7329 0.96 1023 124 0.2271 0.2522 REMARK 3 16 1.7329 - 1.6960 0.96 1004 125 0.2134 0.2410 REMARK 3 17 1.6960 - 1.6621 0.94 984 128 0.2033 0.2418 REMARK 3 18 1.6621 - 1.6307 0.94 958 137 0.2175 0.2375 REMARK 3 19 1.6307 - 1.6016 0.93 976 143 0.2070 0.2380 REMARK 3 20 1.6016 - 1.5745 0.92 939 130 0.2117 0.2789 REMARK 3 21 1.5745 - 1.5491 0.92 953 134 0.2270 0.2585 REMARK 3 22 1.5491 - 1.5252 0.92 944 121 0.2350 0.2581 REMARK 3 23 1.5252 - 1.5028 0.88 904 134 0.2297 0.3402 REMARK 3 24 1.5028 - 1.4816 0.84 858 124 0.2511 0.2773 REMARK 3 25 1.4816 - 1.4616 0.72 744 104 0.2852 0.3315 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 : 0.42 REMARK 3 B_SOL : 50.94 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03330 REMARK 3 B22 (A**2) : 0.03330 REMARK 3 B33 (A**2) : -0.06670 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 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 : 0.007 1254 REMARK 3 ANGLE : 1.174 1674 REMARK 3 CHIRALITY : 0.072 167 REMARK 3 PLANARITY : 0.006 219 REMARK 3 DIHEDRAL : 17.076 483 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: NULL REMARK 4 REMARK 4 2ZQT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000028309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : CN1707 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29561 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 1PIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 69.04550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.48300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.48300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 103.56825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.48300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.48300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.52275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.48300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.48300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 103.56825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.48300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.48300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.52275 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 69.04550 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 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 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 4 REMARK 465 GLU A 5 REMARK 465 ASN A 40 REMARK 465 SER A 41 REMARK 465 SER A 42 REMARK 465 SER A 43 REMARK 465 GLY A 44 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 LEU A 7 143.61 69.32 REMARK 500 SER A 18 -2.39 53.13 REMARK 500 SER A 19 -149.18 -134.61 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 SO4 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PG A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZQS RELATED DB: PDB REMARK 900 RELATED ID: 2ZQU RELATED DB: PDB REMARK 900 RELATED ID: 2ZQV RELATED DB: PDB REMARK 900 RELATED ID: 1PIN RELATED DB: PDB DBREF 2ZQT A 1 163 UNP Q13526 PIN1_HUMAN 1 163 SEQADV 2ZQT ALA A 130 UNP Q13526 MET 130 ENGINEERED MUTATION SEQRES 1 A 163 MET ALA ASP GLU GLU LYS LEU PRO PRO GLY TRP GLU LYS SEQRES 2 A 163 ARG MET SER ARG SER SER GLY ARG VAL TYR TYR PHE ASN SEQRES 3 A 163 HIS ILE THR ASN ALA SER GLN TRP GLU ARG PRO SER GLY SEQRES 4 A 163 ASN SER SER SER GLY GLY LYS ASN GLY GLN GLY GLU PRO SEQRES 5 A 163 ALA ARG VAL ARG CYS SER HIS LEU LEU VAL LYS HIS SER SEQRES 6 A 163 GLN SER ARG ARG PRO SER SER TRP ARG GLN GLU LYS ILE SEQRES 7 A 163 THR ARG THR LYS GLU GLU ALA LEU GLU LEU ILE ASN GLY SEQRES 8 A 163 TYR ILE GLN LYS ILE LYS SER GLY GLU GLU ASP PHE GLU SEQRES 9 A 163 SER LEU ALA SER GLN PHE SER ASP CYS SER SER ALA LYS SEQRES 10 A 163 ALA ARG GLY ASP LEU GLY ALA PHE SER ARG GLY GLN ALA SEQRES 11 A 163 GLN LYS PRO PHE GLU ASP ALA SER PHE ALA LEU ARG THR SEQRES 12 A 163 GLY GLU MET SER GLY PRO VAL PHE THR ASP SER GLY ILE SEQRES 13 A 163 HIS ILE ILE LEU ARG THR GLU HET SO4 A 400 5 HET 1PG A 300 17 HETNAM SO4 SULFATE ION HETNAM 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)- HETNAM 2 1PG ETHANOL FORMUL 2 SO4 O4 S 2- FORMUL 3 1PG C11 H24 O6 FORMUL 4 HOH *179(H2 O) HELIX 1 1 THR A 81 GLY A 99 1 19 HELIX 2 2 ASP A 102 SER A 111 1 10 HELIX 3 3 CYS A 113 ARG A 119 5 7 HELIX 4 4 GLN A 131 LEU A 141 1 11 SHEET 1 A 3 TRP A 11 MET A 15 0 SHEET 2 A 3 VAL A 22 ASN A 26 -1 O TYR A 23 N ARG A 14 SHEET 3 A 3 SER A 32 GLN A 33 -1 O GLN A 33 N TYR A 24 SHEET 1 B 4 ASP A 121 PHE A 125 0 SHEET 2 B 4 VAL A 55 VAL A 62 -1 N CYS A 57 O LEU A 122 SHEET 3 B 4 GLY A 155 GLU A 163 -1 O ILE A 156 N VAL A 62 SHEET 4 B 4 VAL A 150 THR A 152 -1 N VAL A 150 O HIS A 157 SITE 1 AC1 5 LYS A 63 ARG A 68 ARG A 69 SER A 154 SITE 2 AC1 5 HOH A 346 SITE 1 AC2 7 TYR A 23 SER A 32 TRP A 34 GLU A 35 SITE 2 AC2 7 GLY A 48 LYS A 97 HOH A 315 CRYST1 48.966 48.966 138.091 90.00 90.00 90.00 P 43 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 0.020422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020422 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007242 0.00000