PDB Short entry for 2MF9 HEADER APOPTOSIS, ISOMERASE 08-OCT-13 2MF9 TITLE SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN FKBP38 TITLE 2 (FKBP38NTD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 58-206; COMPND 5 SYNONYM: PPIASE FKBP8, 38 KDA FK506-BINDING PROTEIN, 38 KDA FKBP, COMPND 6 FKBP-38, HFKBP38, FK506-BINDING PROTEIN 8, FKBP-8, FKBPR38, ROTAMASE; COMPND 7 EC: 5.2.1.8; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FKBP8, FKBP38; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET29 KEYWDS BETA BARREL, CENTRAL HELIX, FLEXIBLE N-TERMINAL EXTENSION, APOPTOSIS, KEYWDS 2 ISOMERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.KANG,H.YE,B.SIMON,M.SATTLER,H.S.YOON REVDAT 1 06-NOV-13 2MF9 0 SPRSDE 06-NOV-13 2MF9 2JWX JRNL AUTH C.KANG,H.YE,J.CHIA,B.H.CHOI,S.DHE-PAGANON,B.SIMON,U.SCHUTZ, JRNL AUTH 2 M.SATTLER,H.S.YOON JRNL TITL FUNCTIONAL ROLE OF THE FLEXIBLE N-TERMINAL EXTENSION OF JRNL TITL 2 FKBP38 IN CATALYSIS. JRNL REF SCI REP V. 3 2985 2013 JRNL REFN ESSN 2045-2322 JRNL PMID 24145868 JRNL DOI 10.1038/SREP02985 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.B.KANG,H.YE,S.VIVEKANANDAN,B.SIMON,M.SATTLER,H.S.YOON REMARK 1 TITL BACKBONE 1H, 13C, AND 15N RESONANCE ASSIGNMENTS OF THE REMARK 1 TITL 2 N-TERMINAL DOMAIN OF FKBP38 (FKBP38NTD). REMARK 1 REF J.BIOMOL.NMR V.PL 1 37 2006 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 16718587 REMARK 1 DOI 10.1007/S10858-006-9001-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, CNS 1.1 REMARK 3 AUTHORS : LINGE, O'DONOGHUE, NILGES (ARIA), BRUNGER, ADAMS, REMARK 3 CLORE, GROS, NILGES, READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-OCT-13. REMARK 100 THE RCSB ID CODE IS RCSB103557. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1 MM [U-15N] FKBP38-1, 20 MM REMARK 210 NA-PO4-2, 50 MM NACL-3, 1 MM DTT- REMARK 210 4, 0.1 MM EDTA-5, 10 % [U-99% 2H] REMARK 210 D2O-6, 90% H2O/10% D2O; 0.5-1 MM REMARK 210 [U-13C; U-15N] FKBP38-7, 20 MM NA REMARK 210 -PO4-8, 50 MM NACL-9, 1 MM DTT- REMARK 210 10, 0.1 MM EDTA-11, 10 % [U-99% REMARK 210 2H] D2O-12, 0.5-1 MM [U-13C; U- REMARK 210 15N] FKBP38-13, 20 MM NA-PO4-14, REMARK 210 50 MM NACL-15, 1 MM DTT-16, 0.1 REMARK 210 MM EDTA-17, 100 % [U-100% 2H] D2O REMARK 210 -18, 90% H2O/10% D2O; 0.5-1 MM [U REMARK 210 -13C; U-15N] FKBP38-19, 20 MM NA- REMARK 210 PO4-20, 50 MM NACL-21, 1 MM DTT- REMARK 210 22, 0.1 MM EDTA-23, 10 % [U-99% REMARK 210 2H] D2O-24, 0.5-1 MM [U-13C; U- REMARK 210 15N] FKBP38-25, 20 MM NA-PO4-26, REMARK 210 50 MM NACL-27, 1 MM DTT-28, 0.1 REMARK 210 MM EDTA-29, 100 % [U-100% 2H] D2O REMARK 210 -30, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H15N_HSQC; 3D_HNCA; 3D_HN(CO) REMARK 210 CA; 3D_HNCO; 3D_HNCACB; 3D_ REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 H(CCO)NH; 3D C(CO)NH; 2D 1H-1H REMARK 210 NOESY; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D 1H-13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, NMRPIPE 2.3, FELIX_ REMARK 210 FELIX2004 FELIX2004, NMRVIEW 5.2.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 HG21 THR A 67 HG21 VAL A 87 1.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 12 TYR A 131 CE1 TYR A 131 CZ 0.081 REMARK 500 12 TYR A 131 CZ TYR A 131 CE2 -0.086 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 ALA A 9 -174.81 69.33 REMARK 500 1 GLU A 10 -77.17 -127.26 REMARK 500 1 LEU A 15 -47.50 -133.01 REMARK 500 1 ALA A 16 97.43 65.16 REMARK 500 1 ALA A 22 34.12 -148.00 REMARK 500 1 ALA A 30 80.55 60.83 REMARK 500 1 PRO A 31 96.02 -66.63 REMARK 500 1 GLU A 34 -55.86 71.20 REMARK 500 1 PRO A 52 57.05 -107.79 REMARK 500 1 PRO A 55 -159.21 -94.49 REMARK 500 1 GLU A 85 113.28 -166.34 REMARK 500 1 VAL A 95 -157.07 -140.04 REMARK 500 1 CYS A 121 -92.03 -119.72 REMARK 500 1 TYR A 122 43.62 -142.02 REMARK 500 1 TYR A 131 98.02 -58.85 REMARK 500 1 HIS A 135 28.76 47.59 REMARK 500 1 LEU A 150 10.02 -141.50 REMARK 500 1 HIS A 152 16.98 -143.05 REMARK 500 1 HIS A 154 -172.27 64.87 REMARK 500 2 PRO A 12 -79.35 -82.54 REMARK 500 2 ALA A 14 32.63 -83.60 REMARK 500 2 ALA A 22 145.52 72.70 REMARK 500 2 ALA A 30 -56.63 -171.03 REMARK 500 2 PRO A 52 64.77 -104.28 REMARK 500 2 GLU A 85 105.58 -161.50 REMARK 500 2 VAL A 95 -153.94 -139.87 REMARK 500 2 CYS A 121 -92.34 -122.78 REMARK 500 2 TYR A 122 37.66 -147.37 REMARK 500 2 TYR A 131 97.45 -55.57 REMARK 500 2 LEU A 150 22.94 -152.95 REMARK 500 2 GLU A 151 -96.04 -72.83 REMARK 500 2 HIS A 152 68.32 37.53 REMARK 500 2 HIS A 153 8.75 -67.47 REMARK 500 3 GLU A 10 25.76 -140.60 REMARK 500 3 LEU A 15 -165.19 69.13 REMARK 500 3 ARG A 17 32.13 -144.11 REMARK 500 3 GLU A 18 92.53 -68.89 REMARK 500 3 ALA A 30 71.09 -159.40 REMARK 500 3 PRO A 31 101.04 -51.39 REMARK 500 3 GLU A 34 -55.66 179.54 REMARK 500 3 GLU A 35 110.35 69.33 REMARK 500 3 TRP A 36 -157.32 -109.84 REMARK 500 3 PRO A 52 53.66 -104.61 REMARK 500 3 GLU A 85 110.83 -164.94 REMARK 500 3 VAL A 95 -156.87 -133.96 REMARK 500 3 CYS A 121 -89.44 -122.56 REMARK 500 3 TYR A 122 40.67 -143.88 REMARK 500 3 TYR A 131 97.97 -55.95 REMARK 500 3 LEU A 150 25.44 -161.45 REMARK 500 3 GLU A 151 -71.72 -72.68 REMARK 500 REMARK 500 THIS ENTRY HAS 331 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 18 TYR A 120 0.05 SIDE CHAIN REMARK 500 20 TYR A 120 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED SHEET 6 & 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6923 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM 2 OF DATABASE Q14318 REMARK 999 (FKBP8_HUMAN). DBREF 2MF9 A 1 149 UNP Q14318 FKBP8_HUMAN 58 206 SEQADV 2MF9 LEU A 150 UNP Q14318 EXPRESSION TAG SEQADV 2MF9 GLU A 151 UNP Q14318 EXPRESSION TAG SEQADV 2MF9 HIS A 152 UNP Q14318 EXPRESSION TAG SEQADV 2MF9 HIS A 153 UNP Q14318 EXPRESSION TAG SEQADV 2MF9 HIS A 154 UNP Q14318 EXPRESSION TAG SEQADV 2MF9 HIS A 155 UNP Q14318 EXPRESSION TAG SEQADV 2MF9 HIS A 156 UNP Q14318 EXPRESSION TAG SEQADV 2MF9 HIS A 157 UNP Q14318 EXPRESSION TAG SEQRES 1 A 157 MET GLY GLN PRO PRO ALA GLU GLU ALA GLU GLN PRO GLY SEQRES 2 A 157 ALA LEU ALA ARG GLU PHE LEU ALA ALA MET GLU PRO GLU SEQRES 3 A 157 PRO ALA PRO ALA PRO ALA PRO GLU GLU TRP LEU ASP ILE SEQRES 4 A 157 LEU GLY ASN GLY LEU LEU ARG LYS LYS THR LEU VAL PRO SEQRES 5 A 157 GLY PRO PRO GLY SER SER ARG PRO VAL LYS GLY GLN VAL SEQRES 6 A 157 VAL THR VAL HIS LEU GLN THR SER LEU GLU ASN GLY THR SEQRES 7 A 157 ARG VAL GLN GLU GLU PRO GLU LEU VAL PHE THR LEU GLY SEQRES 8 A 157 ASP CYS ASP VAL ILE GLN ALA LEU ASP LEU SER VAL PRO SEQRES 9 A 157 LEU MET ASP VAL GLY GLU THR ALA MET VAL THR ALA ASP SEQRES 10 A 157 SER LYS TYR CYS TYR GLY PRO GLN GLY SER ARG SER PRO SEQRES 11 A 157 TYR ILE PRO PRO HIS ALA ALA LEU CYS LEU GLU VAL THR SEQRES 12 A 157 LEU LYS THR ALA VAL ASP LEU GLU HIS HIS HIS HIS HIS SEQRES 13 A 157 HIS HELIX 1 1 ILE A 96 VAL A 103 1 8 HELIX 2 2 LYS A 119 CYS A 121 5 3 SHEET 1 A 7 LEU A 37 ASP A 38 0 SHEET 2 A 7 LEU A 45 VAL A 51 -1 O LYS A 47 N LEU A 37 SHEET 3 A 7 THR A 111 ASP A 117 -1 O MET A 113 N LYS A 48 SHEET 4 A 7 ALA A 137 VAL A 148 -1 O LEU A 140 N VAL A 114 SHEET 5 A 7 VAL A 65 SER A 73 -1 N SER A 73 O CYS A 139 SHEET 6 A 7 VAL A 80 GLU A 83 -1 SHEET 7 A 7 LEU A 86 THR A 89 -1 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