HEADER ISOMERASE 10-JUN-13 2M9I TITLE NMR SOLUTION STRUCTURE OF PIN1 WW DOMAIN VARIANT 6-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MODIFIED WW DOMAIN (UNP RESIDUES 6-39); COMPND 5 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PIN1, PPIASE PIN1, COMPND 6 ROTAMASE PIN1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS N-GLYCOSYLATION, ENHANCED AROMATIC SEQUON, WW DOMAIN, CH-PI KEYWDS 2 INTERACTION, ISOMERASE EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR S.ENCK,W.CHEN,J.L.PRICE,E.T.POWERS,C.WONG,H.J.DYSON,J.W.KELLY REVDAT 4 14-JUN-23 2M9I 1 REMARK REVDAT 3 17-JUL-13 2M9I 1 JRNL REVDAT 2 03-JUL-13 2M9I 1 JRNL REVDAT 1 26-JUN-13 2M9I 0 JRNL AUTH W.CHEN,S.ENCK,J.L.PRICE,D.L.POWERS,E.T.POWERS,C.H.WONG, JRNL AUTH 2 H.J.DYSON,J.W.KELLY JRNL TITL STRUCTURAL AND ENERGETIC BASIS OF CARBOHYDRATE-AROMATIC JRNL TITL 2 PACKING INTERACTIONS IN PROTEINS. JRNL REF J.AM.CHEM.SOC. V. 135 9877 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23742246 JRNL DOI 10.1021/JA4040472 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), CASE, DARDEN, REMARK 3 CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, ... REMARK 3 AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000103378. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.08 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 500 UM PIN WW DOMAIN PEPTIDE, 50 REMARK 210 MM SODIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 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 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 OD1 ASN A 14 HG1 THR A 16 1.57 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 3 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 PRO A 3 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 9 PRO A 3 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 9 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 PRO A 3 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 12 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 13 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 16 ARG A 31 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 18 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 19 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.6 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 14 -32.18 -143.09 REMARK 500 2 SER A 13 -4.42 78.46 REMARK 500 2 ASN A 14 -29.15 -141.88 REMARK 500 2 SER A 33 13.22 -142.76 REMARK 500 3 SER A 13 -1.93 73.04 REMARK 500 3 ASN A 14 -22.49 -141.44 REMARK 500 3 HIS A 22 1.61 -69.07 REMARK 500 4 SER A 13 -7.95 90.14 REMARK 500 4 ASN A 14 -24.21 -141.36 REMARK 500 4 ASN A 25 6.86 83.99 REMARK 500 4 PRO A 32 -157.60 -73.57 REMARK 500 4 SER A 33 15.68 -61.74 REMARK 500 5 SER A 13 -6.03 90.31 REMARK 500 5 ASN A 14 -29.09 -149.20 REMARK 500 5 PRO A 32 -165.76 -75.59 REMARK 500 6 SER A 13 -7.54 73.90 REMARK 500 6 ASN A 25 7.30 84.62 REMARK 500 7 SER A 13 -22.86 90.23 REMARK 500 7 ASN A 14 -28.38 -145.79 REMARK 500 7 ASN A 25 1.07 80.24 REMARK 500 8 ASN A 14 -30.74 -144.55 REMARK 500 8 HIS A 22 1.71 -69.76 REMARK 500 8 SER A 33 45.97 -171.09 REMARK 500 9 ASN A 14 -31.07 -143.31 REMARK 500 10 SER A 13 -9.70 90.55 REMARK 500 10 ASN A 14 -28.19 -146.85 REMARK 500 10 PRO A 32 -168.99 -71.34 REMARK 500 10 SER A 33 -52.80 67.43 REMARK 500 11 ASN A 14 -31.17 -143.93 REMARK 500 12 SER A 13 -6.51 90.41 REMARK 500 12 ASN A 14 -25.11 -143.44 REMARK 500 12 SER A 33 39.02 -161.88 REMARK 500 13 SER A 13 -12.30 90.22 REMARK 500 13 ASN A 14 -22.83 -144.25 REMARK 500 13 ASN A 25 6.46 82.67 REMARK 500 13 PRO A 32 -159.89 -75.01 REMARK 500 13 SER A 33 15.82 -61.22 REMARK 500 14 SER A 13 -20.46 90.28 REMARK 500 14 ASN A 14 -31.55 -145.01 REMARK 500 14 HIS A 22 3.71 -69.52 REMARK 500 14 ASN A 25 2.94 83.30 REMARK 500 15 SER A 13 -9.18 82.29 REMARK 500 15 ASN A 14 -21.20 -141.56 REMARK 500 15 SER A 33 -73.52 141.96 REMARK 500 16 SER A 13 -11.78 90.89 REMARK 500 16 ASN A 14 -23.59 -144.55 REMARK 500 16 ASN A 25 1.37 80.71 REMARK 500 16 SER A 33 18.35 -165.75 REMARK 500 17 SER A 13 -20.11 90.32 REMARK 500 17 ASN A 14 -31.24 -145.24 REMARK 500 REMARK 500 THIS ENTRY HAS 61 RAMACHANDRAN OUTLIERS. 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 31 0.12 SIDE CHAIN REMARK 500 10 ARG A 31 0.10 SIDE CHAIN REMARK 500 17 ARG A 12 0.11 SIDE CHAIN REMARK 500 17 ARG A 31 0.10 SIDE CHAIN REMARK 500 18 ARG A 12 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19295 RELATED DB: BMRB REMARK 900 RELATED ID: 2M9E RELATED DB: PDB REMARK 900 RELATED ID: 2M9F RELATED DB: PDB REMARK 900 RELATED ID: 2M9J RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS IS A PIN1 WW DOMAIN VARIANT DBREF 2M9I A 1 34 UNP Q13526 PIN1_HUMAN 6 39 SEQADV 2M9I PHE A 11 UNP Q13526 SER 16 SEE REMARK 999 SEQADV 2M9I ASN A 14 UNP Q13526 SER 19 SEE REMARK 999 SEQADV 2M9I THR A 16 UNP Q13526 ARG 21 SEE REMARK 999 SEQADV 2M9I PHE A 29 UNP Q13526 TRP 34 SEE REMARK 999 SEQRES 1 A 34 LYS LEU PRO PRO GLY TRP GLU LYS ARG MET PHE ARG SER SEQRES 2 A 34 ASN GLY THR VAL TYR TYR PHE ASN HIS ILE THR ASN ALA SEQRES 3 A 34 SER GLN PHE GLU ARG PRO SER GLY SHEET 1 A 3 TRP A 6 MET A 10 0 SHEET 2 A 3 VAL A 17 ASN A 21 -1 O TYR A 18 N ARG A 9 SHEET 3 A 3 SER A 27 GLN A 28 -1 O GLN A 28 N TYR A 19 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