HEADER ISOMERASE 11-SEP-07 2JV4 TITLE STRUCTURE CHARACTERISATION OF PINA WW DOMAIN AND COMPARISON WITH OTHER TITLE 2 GROUP IV WW DOMAINS, PIN1 AND ESS1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS/TRANS ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WW DOMAIN, RESIDUES UNP 1-52; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EMERICELLA NIDULANS; SOURCE 3 ORGANISM_TAXID: 162425; SOURCE 4 GENE: PINA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS PPIASE DOMAIN, WW DOMAIN GROUP IV, ISOMERASE, ROTAMASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.A.NG,Y.KATO,M.TANOKURA,R.T.C.BROWNLEE REVDAT 5 16-MAR-22 2JV4 1 REMARK SEQADV REVDAT 4 24-FEB-09 2JV4 1 VERSN REVDAT 3 26-AUG-08 2JV4 1 JRNL REVDAT 2 23-OCT-07 2JV4 1 SPRSDE REVDAT 1 16-OCT-07 2JV4 0 SPRSDE 23-OCT-07 2JV4 2JM7 JRNL AUTH C.A.NG,Y.KATO,M.TANOKURA,R.T.C.BROWNLEE JRNL TITL STRUCTURAL CHARACTERISATION OF PINA WW DOMAIN AND A JRNL TITL 2 COMPARISON WITH OTHER GROUP IV WW DOMAINS, PIN1 AND ESS1 JRNL REF BIOCHIM.BIOPHYS.ACTA V.1784 1208 2008 JRNL REFN ISSN 0006-3002 JRNL PMID 18503784 JRNL DOI 10.1016/J.BBAPAP.2008.04.026 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER 9 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 KOLL (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ENERGY MINIMISASTION SUBJECT TO NMR REMARK 3 CONSTRAINTS REMARK 4 REMARK 4 2JV4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000100328. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.8MM [U-100% 13C; U-100% 15N] REMARK 210 PEPTIDYL-PROLYL CIS/TRANS REMARK 210 ISOMERASE, 50MM SODIUM PHOSPHATE, REMARK 210 50MM SODIUM CHLORIDE, 0.02% REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNHA; 3D_13C- SEPARATED_ REMARK 210 NOESY; 3D_15N- SEPARATED_ NOESY; REMARK 210 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HN(COCA)CB; 3D HCCH-COSY; 3D REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY 3, VNMR, TALOS, REMARK 210 AMBER 9 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 7 LEU A 45 CB - CG - CD1 ANGL. DEV. = 12.6 DEGREES REMARK 500 8 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 8 LEU A 45 CB - CG - CD1 ANGL. DEV. = 10.6 DEGREES REMARK 500 10 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 11 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 LEU A 45 CB - CG - CD1 ANGL. DEV. = 11.6 DEGREES REMARK 500 12 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 13 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 17 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 18 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 LEU A 45 CB - CG - CD1 ANGL. DEV. = 11.4 DEGREES REMARK 500 20 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 20 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES 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 1 GLU A 12 99.16 174.42 REMARK 500 1 MET A 42 -42.44 -25.97 REMARK 500 2 PRO A 8 -153.86 -77.48 REMARK 500 2 ASN A 17 135.70 174.85 REMARK 500 2 ASN A 20 24.52 -79.16 REMARK 500 2 TRP A 34 -17.16 -144.50 REMARK 500 2 MET A 42 -35.88 -37.83 REMARK 500 2 TYR A 48 -70.03 -104.11 REMARK 500 2 ALA A 50 60.30 -162.50 REMARK 500 2 THR A 51 91.20 -25.94 REMARK 500 3 PRO A 8 -150.82 -78.67 REMARK 500 3 SER A 16 108.09 -51.19 REMARK 500 3 ASN A 17 140.78 152.26 REMARK 500 3 LYS A 19 -166.17 -79.10 REMARK 500 3 ARG A 30 104.56 -47.18 REMARK 500 3 TRP A 34 -18.28 -142.54 REMARK 500 3 ASP A 41 53.42 -107.88 REMARK 500 3 MET A 42 -40.38 -27.20 REMARK 500 4 PRO A 8 -158.34 -75.80 REMARK 500 4 TRP A 11 -2.47 -141.64 REMARK 500 4 ARG A 30 101.12 -50.36 REMARK 500 4 TRP A 34 -36.33 -130.62 REMARK 500 4 ASP A 41 60.27 -119.09 REMARK 500 4 TYR A 48 -56.25 -121.27 REMARK 500 5 MET A 2 145.49 166.04 REMARK 500 5 PRO A 8 -141.45 -77.24 REMARK 500 5 HIS A 15 137.60 -172.39 REMARK 500 5 ASP A 41 48.43 -107.09 REMARK 500 5 MET A 42 -43.19 -29.38 REMARK 500 5 TYR A 48 -58.35 -135.42 REMARK 500 6 GLU A 12 140.85 175.73 REMARK 500 6 ARG A 30 97.89 -65.00 REMARK 500 6 ASP A 41 56.57 -115.17 REMARK 500 7 PRO A 8 -147.15 -77.95 REMARK 500 7 ASN A 20 46.67 -88.10 REMARK 500 7 ARG A 30 103.10 -32.70 REMARK 500 7 MET A 42 -40.05 60.99 REMARK 500 7 MET A 47 18.31 -69.87 REMARK 500 7 TYR A 48 -32.38 -138.28 REMARK 500 8 PRO A 8 -152.23 -77.30 REMARK 500 8 MET A 42 -45.39 -5.35 REMARK 500 9 GLU A 12 124.96 174.72 REMARK 500 9 ASN A 20 32.78 -82.17 REMARK 500 9 THR A 29 130.31 -174.27 REMARK 500 9 GLU A 31 -180.00 -170.98 REMARK 500 9 ASP A 41 48.30 -105.14 REMARK 500 9 MET A 42 -47.20 -22.07 REMARK 500 9 TYR A 48 -61.75 -107.20 REMARK 500 10 PRO A 8 -149.50 -80.52 REMARK 500 10 ALA A 9 4.65 -63.24 REMARK 500 REMARK 500 THIS ENTRY HAS 92 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 49 ALA A 50 17 148.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 ARG A 14 0.09 SIDE CHAIN REMARK 500 12 ARG A 33 0.10 SIDE CHAIN REMARK 500 13 TYR A 24 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2JV4 A 2 53 UNP O42735 O42735_EMENI 1 52 SEQADV 2JV4 GLY A 0 UNP O42735 EXPRESSION TAG SEQADV 2JV4 SER A 1 UNP O42735 EXPRESSION TAG SEQRES 1 A 54 GLY SER MET VAL ASN THR GLY LEU PRO ALA GLY TRP GLU SEQRES 2 A 54 VAL ARG HIS SER ASN SER LYS ASN LEU PRO TYR TYR PHE SEQRES 3 A 54 ASN PRO ALA THR ARG GLU SER ARG TRP GLU PRO PRO ALA SEQRES 4 A 54 ASP THR ASP MET GLU THR LEU LYS MET TYR MET ALA THR SEQRES 5 A 54 TYR HIS HELIX 1 1 ASP A 41 ALA A 50 1 10 SHEET 1 A 3 VAL A 13 HIS A 15 0 SHEET 2 A 3 PRO A 22 ASN A 26 -1 O TYR A 23 N ARG A 14 SHEET 3 A 3 GLU A 31 ARG A 33 -1 O ARG A 33 N TYR A 24 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1