10 20 30 40 50 60 70 80 2KBU - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ISOMERASE 08-DEC-08 2KBU
TITLE NMR SOLUTION STRUCTURE OF PIN1 WW DOMAIN MUTANT WITH BETA TITLE 2 TURN MIMIC AT POSITION 12
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA- COMPND 3 INTERACTING 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 6-39; COMPND 6 SYNONYM: ROTAMASE PIN1, PPIASE PIN1; COMPND 7 EC: 5.2.1.8; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: RESIDUES RSSG REPLACED BY THE BETA-TURN COMPND 11 MIMIC CFD
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RESIDUES RSSG REPLACED BY THE BETA-TURN SOURCE 4 MIMIC CFD
KEYWDS BETA SHEET NUCLEATOR, BETA TURN MIMIC, CELL CYCLE, KEYWDS 2 ISOMERASE, NUCLEUS, PHOSPHOPROTEIN, ROTAMASE
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR A.A.FULLER,G.BHABHA,D.A.CASE
REVDAT 2 28-JUL-09 2KBU 1 JRNL REVDAT 1 07-JUL-09 2KBU 0
JRNL AUTH A.A.FULLER,D.DU,F.LIU,J.E.DAVOREN,G.BHABHA,G.KROON, JRNL AUTH 2 D.A.CASE,H.J.DYSON,E.T.POWERS,P.WIPF,M.GRUEBELE, JRNL AUTH 3 J.W.KELLY JRNL TITL EVALUATING BETA-TURN MIMICS AS BETA-SHEET FOLDING JRNL TITL 2 NUCLEATORS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 11067 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19541614 JRNL DOI 10.1073/PNAS.0813012106
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KBU COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-08. REMARK 100 THE RCSB ID CODE IS RCSB100926.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288.2 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.446 MM WW DOMAIN, 90% H2O/ REMARK 210 10% D2O; 0.447 MM WW DOMAIN, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H REMARK 210 COSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 27 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 001 REMARK 210 REMARK 210 REMARK: SAME EXPERIMENTS ALSO COLLECTED IN D2O WITH SAMPLE-2
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 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 9 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 PRO A 29 CA - N - CD ANGL. DEV. = -11.0 DEGREES REMARK 500 3 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 28 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 8 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 9 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 11 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 12 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 12 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 ARG A 28 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 14 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 15 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 15 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.0 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 ASN A 22 -8.60 59.79 REMARK 500 1 PRO A 29 -166.91 -72.97 REMARK 500 2 PRO A 29 61.43 25.62 REMARK 500 3 PRO A 3 176.13 -58.61 REMARK 500 3 PRO A 4 177.82 -59.81 REMARK 500 4 ILE A 20 -50.48 -126.76 REMARK 500 4 ASN A 22 -11.32 57.60 REMARK 500 4 PRO A 29 -165.06 -74.06 REMARK 500 5 PRO A 3 172.98 -54.76 REMARK 500 5 PRO A 4 179.56 -57.51 REMARK 500 5 PRO A 29 48.55 -68.98 REMARK 500 5 SER A 30 -17.00 59.40 REMARK 500 7 PRO A 4 -177.35 -64.58 REMARK 500 7 ASN A 22 5.02 59.76 REMARK 500 7 PRO A 29 172.64 -54.18 REMARK 500 7 SER A 30 37.78 -71.19 REMARK 500 8 PRO A 4 -169.75 -63.77 REMARK 500 8 ASN A 22 6.62 59.83 REMARK 500 8 PRO A 29 -142.82 -73.94 REMARK 500 8 SER A 30 48.15 -64.38 REMARK 500 9 ASN A 22 19.44 52.86 REMARK 500 9 ARG A 28 63.46 34.46 REMARK 500 9 SER A 30 6.57 48.01 REMARK 500 10 PRO A 4 151.97 -47.02 REMARK 500 10 ASN A 22 6.58 54.49 REMARK 500 10 ARG A 28 151.27 60.81 REMARK 500 10 PRO A 29 141.61 -22.94 REMARK 500 10 SER A 30 87.63 -55.55 REMARK 500 11 ASN A 22 -4.17 61.02 REMARK 500 12 ASN A 22 -12.33 60.81 REMARK 500 13 ASN A 22 -10.20 61.61 REMARK 500 13 SER A 30 46.84 -158.92 REMARK 500 14 ILE A 20 -62.40 -109.42 REMARK 500 15 ASN A 22 17.27 53.04 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 6 ARG A 28 0.08 SIDE_CHAIN REMARK 500 12 ARG A 28 0.12 SIDE_CHAIN REMARK 500 14 ARG A 28 0.09 SIDE_CHAIN REMARK 500 15 ARG A 28 0.08 SIDE_CHAIN 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 CFD A 12
REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES RSSG REPLACED BY THE BETA-TURN MIMIC CFD
DBREF 2KBU A 1 31 UNP Q13526 PIN1_HUMAN 6 39
SEQADV 2KBU A UNP Q13526 ARG 17 SEE REMARK 999 SEQADV 2KBU A UNP Q13526 SER 18 SEE REMARK 999 SEQADV 2KBU A UNP Q13526 SER 19 SEE REMARK 999 SEQADV 2KBU CFD A 12 UNP Q13526 GLY 20 SEE REMARK 999 SEQADV 2KBU PHE A 26 UNP Q13526 TRP 34 ENGINEERED
SEQRES 1 A 31 LYS LEU PRO PRO GLY TRP GLU LYS ARG MET SER CFD ARG SEQRES 2 A 31 VAL TYR TYR PHE ASN HIS ILE THR ASN ALA SER GLN PHE SEQRES 3 A 31 GLU ARG PRO SER GLY
HET CFD A 12 14
HETNAM CFD (2R,3E,5R)-5-AMINO-2,4-DIMETHYLHEX-3-ENAL
FORMUL 1 CFD C8 H15 N O
SHEET 1 A 3 TRP A 6 MET A 10 0 SHEET 2 A 3 VAL A 14 ASN A 18 -1 O TYR A 15 N ARG A 9 SHEET 3 A 3 SER A 24 GLN A 25 -1 O GLN A 25 N TYR A 16
LINK C SER A 11 N CFD A 12 1555 1555 1.34 LINK C CFD A 12 N ARG A 13 1555 1555 1.34
SITE 1 AC1 3 MET A 10 SER A 11 ARG A 13
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