HEADER ISOMERASE 22-AUG-08 2ZR4
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: ROTAMASE PIN1, PPIASE PIN1;
COMPND 5 EC: 5.2.1.8;
COMPND 6 ENGINEERED: YES;
COMPND 7 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 (S32A), ISOMERASE, CELL CYCLE, NUCLEUS, PHOSPHOPROTEIN,
KEYWDS 2 ROTAMASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.JOBICHEN,L.YIH-CHERNG,J.SIVARAMAN
REVDAT 3 01-NOV-23 2ZR4 1 REMARK
REVDAT 2 10-NOV-21 2ZR4 1 REMARK SEQADV
REVDAT 1 25-AUG-09 2ZR4 0
JRNL AUTH C.JOBICHEN,L.YIH-CHERNG,J.SIVARAMAN
JRNL TITL STRUCTURAL STUDIES ON PIN1 MUTANTS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 11718
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 SET) : 0.237
REMARK 3 FREE R VALUE : 0.266
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 757
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1211
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 22
REMARK 3 SOLVENT ATOMS : 139
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 1.330
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2ZR4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-08.
REMARK 100 THE DEPOSITION ID IS D_1000028320.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-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 : 15430
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
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 (%) : 94.6
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06200
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000
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: PDB ENTRY 1PIN
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5M AMMONIUM SULFATE, 100MM HEPES
REMARK 280 -NA(PH7.5), 2% PEG400, 2MM DTT, 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 69.88250
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.29300
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.29300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.82375
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.29300
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.29300
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.94125
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.29300
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.29300
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 104.82375
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.29300
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.29300
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.94125
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 69.88250
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 7 146.41 67.71
REMARK 500 SER A 18 16.62 50.65
REMARK 500 PRO A 70 56.18 -66.76
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 1PG A 300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 400
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1PIN RELATED DB: PDB
REMARK 900 THIS STRUCTURE IS SIMILAR TO 1PIN EXCEPT THE MUTATION OF SERINE 32
REMARK 900 TO ALANINE
REMARK 900 RELATED ID: 2ZR5 RELATED DB: PDB
REMARK 900 RELATED ID: 2ZR6 RELATED DB: PDB
DBREF 2ZR4 A 1 163 UNP Q13526 PIN1_HUMAN 1 163
SEQADV 2ZR4 ALA A 32 UNP Q13526 SER 32 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 ALA 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 MET
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 1PG A 300 17
HET SO4 A 400 5
HETNAM 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-
HETNAM 2 1PG ETHANOL
HETNAM SO4 SULFATE ION
FORMUL 2 1PG C11 H24 O6
FORMUL 3 SO4 O4 S 2-
FORMUL 4 HOH *139(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 ALA 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 VAL A 55 O PHE A 125
SHEET 3 B 4 ILE A 156 GLU A 163 -1 O LEU A 160 N SER A 58
SHEET 4 B 4 VAL A 150 PHE A 151 -1 N VAL A 150 O HIS A 157
SITE 1 AC1 12 SER A 16 TYR A 23 ASN A 30 ALA A 32
SITE 2 AC1 12 TRP A 34 ILE A 93 LYS A 97 MET A 146
SITE 3 AC1 12 SER A 147 GLY A 148 HOH A1042 HOH A1116
SITE 1 AC2 5 LYS A 63 ARG A 68 ARG A 69 SER A 154
SITE 2 AC2 5 HOH A1113
CRYST1 48.586 48.586 139.765 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 0.020582 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020582 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007155 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
