HEADER ISOMERASE 16-JUL-11 2RS4 TITLE NMR STRUCTURE OF STEREO-ARRAY ISOTOPE LABELLED (SAIL) PEPTIDYL-PROLYL TITLE 2 CIS-TRANS ISOMERASE FROM E. COLI (EPPIB) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE B, ROTAMASE B; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: PPIB, B0525, JW0514; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET3A KEYWDS SAIL, ISOMERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.TAKEDA,J.JEE,A.M.ONO,K.OKUMA,T.TERAUCHI,M.KAINOSHO REVDAT 5 15-MAY-24 2RS4 1 REMARK REVDAT 4 14-JUN-23 2RS4 1 REMARK REVDAT 3 21-DEC-16 2RS4 1 TITLE REVDAT 2 05-JUN-13 2RS4 1 JRNL REVDAT 1 12-OCT-11 2RS4 0 JRNL AUTH M.TAKEDA,J.JEE,A.M.ONO,T.TERAUCHI,M.KAINOSHO JRNL TITL HYDROGEN EXCHANGE STUDY ON THE HYDROXYL GROUPS OF SERINE AND JRNL TITL 2 THREONINE RESIDUES IN PROTEINS AND STRUCTURE REFINEMENT JRNL TITL 3 USING NOE RESTRAINTS WITH POLAR SIDE-CHAIN GROUPS JRNL REF J.AM.CHEM.SOC. V. 133 17420 2011 JRNL REFN ISSN 0002-7863 JRNL PMID 21955241 JRNL DOI 10.1021/JA206799V 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 2RS4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000150219. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 0.4 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM SAIL [E-SAIL PHE, E-SAIL REMARK 210 TYR] EPPIB-1, 50 MM SODIUM REMARK 210 PHOSPHATE-2, 1 MM DTT-3, 100 MM REMARK 210 SODIUM CHLORIDE-4, 90% H2O/10% REMARK 210 D2O; 0.3 MM SAIL [Z-SAIL PHE, E- REMARK 210 SAIL TYR] EPPIB-5, 50 MM SODIUM REMARK 210 PHOSPHATE-6, 1 MM DTT-7, 100 MM REMARK 210 SODIUM CHLORIDE-8, 90% H2O/10% REMARK 210 D2O; 0.3 MM SAIL [D-SAIL PHE, D- REMARK 210 SAIL TYR] EPPIB-9, 50 MM SODIUM REMARK 210 PHOSPHATE-10, 1 MM DTT-11, 100 REMARK 210 MM SODIUM CHLORIDE-12, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCA; 3D HNCACB; 3D REMARK 210 HNCO; 3D CBCA(CO)NH; 3D HN(CO)CA; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D HB(CBCG) REMARK 210 HE; 2D HB(CBCGCZ) HZ REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; 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 : 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 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 O ALA A 90 HG SER A 93 1.59 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 2 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 143 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 19 ARG A 143 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 20 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.1 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 PHE A 16 73.73 -103.65 REMARK 500 1 ALA A 20 55.39 -155.00 REMARK 500 1 ASN A 73 8.82 -65.44 REMARK 500 1 ARG A 80 117.13 -38.88 REMARK 500 1 GLN A 89 -38.65 -151.47 REMARK 500 1 THR A 95 -68.64 -90.04 REMARK 500 1 ALA A 96 20.07 -148.32 REMARK 500 1 SER A 111 -61.02 -109.34 REMARK 500 2 PHE A 16 73.79 -102.85 REMARK 500 2 ALA A 20 61.72 -151.89 REMARK 500 2 ASN A 73 -1.81 -58.62 REMARK 500 2 GLN A 89 -57.39 -159.27 REMARK 500 2 THR A 95 -71.55 -87.07 REMARK 500 2 ALA A 96 38.73 -152.90 REMARK 500 2 SER A 111 21.90 -143.77 REMARK 500 2 ALA A 140 163.54 84.55 REMARK 500 3 PHE A 16 74.52 -104.94 REMARK 500 3 ALA A 20 58.55 -149.74 REMARK 500 3 ASN A 37 5.31 -68.27 REMARK 500 3 ASN A 38 17.49 -145.87 REMARK 500 3 ASN A 73 0.21 -60.93 REMARK 500 3 GLN A 89 -40.38 -153.65 REMARK 500 3 THR A 95 -67.82 -91.65 REMARK 500 3 MET A 146 3.07 59.93 REMARK 500 4 PHE A 16 73.82 -104.22 REMARK 500 4 ALA A 20 59.00 -150.03 REMARK 500 4 ASN A 38 50.35 -144.85 REMARK 500 4 GLN A 89 -58.60 -160.12 REMARK 500 4 HIS A 92 46.46 -101.62 REMARK 500 4 THR A 95 -74.19 -54.42 REMARK 500 4 ALA A 96 36.80 -154.74 REMARK 500 5 PHE A 16 74.36 -104.67 REMARK 500 5 ALA A 20 59.43 -149.62 REMARK 500 5 GLN A 89 -47.67 -158.61 REMARK 500 5 THR A 95 -60.09 -91.91 REMARK 500 5 ALA A 96 33.33 -156.49 REMARK 500 5 SER A 111 -59.29 -126.22 REMARK 500 6 PHE A 16 72.90 -107.13 REMARK 500 6 ALA A 20 56.22 -155.52 REMARK 500 6 ASN A 73 39.24 -75.19 REMARK 500 6 GLN A 89 -58.36 -159.56 REMARK 500 6 HIS A 92 35.30 -99.59 REMARK 500 6 THR A 95 -74.78 -88.41 REMARK 500 7 PHE A 16 72.89 -105.11 REMARK 500 7 ALA A 20 57.90 -149.68 REMARK 500 7 ASN A 73 2.64 -60.45 REMARK 500 7 ASN A 78 73.50 -103.73 REMARK 500 7 GLN A 89 -50.21 -161.25 REMARK 500 7 ALA A 96 -5.04 -153.36 REMARK 500 7 ALA A 140 163.46 82.83 REMARK 500 REMARK 500 THIS ENTRY HAS 146 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 TYR A 30 0.07 SIDE CHAIN REMARK 500 10 TYR A 30 0.07 SIDE CHAIN REMARK 500 11 TYR A 30 0.07 SIDE CHAIN REMARK 500 12 TYR A 30 0.09 SIDE CHAIN REMARK 500 20 TYR A 30 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NUL RELATED DB: PDB REMARK 900 RELATED ID: 11451 RELATED DB: BMRB DBREF 2RS4 A 1 164 UNP P23869 PPIB_ECOLI 1 164 SEQRES 1 A 164 MET VAL THR PHE HIS THR ASN HIS GLY ASP ILE VAL ILE SEQRES 2 A 164 LYS THR PHE ASP ASP LYS ALA PRO GLU THR VAL LYS ASN SEQRES 3 A 164 PHE LEU ASP TYR CYS ARG GLU GLY PHE TYR ASN ASN THR SEQRES 4 A 164 ILE PHE HIS ARG VAL ILE ASN GLY PHE MET ILE GLN GLY SEQRES 5 A 164 GLY GLY PHE GLU PRO GLY MET LYS GLN LYS ALA THR LYS SEQRES 6 A 164 GLU PRO ILE LYS ASN GLU ALA ASN ASN GLY LEU LYS ASN SEQRES 7 A 164 THR ARG GLY THR LEU ALA MET ALA ARG THR GLN ALA PRO SEQRES 8 A 164 HIS SER ALA THR ALA GLN PHE PHE ILE ASN VAL VAL ASP SEQRES 9 A 164 ASN ASP PHE LEU ASN PHE SER GLY GLU SER LEU GLN GLY SEQRES 10 A 164 TRP GLY TYR CYS VAL PHE ALA GLU VAL VAL ASP GLY MET SEQRES 11 A 164 ASP VAL VAL ASP LYS ILE LYS GLY VAL ALA THR GLY ARG SEQRES 12 A 164 SER GLY MET HIS GLN ASP VAL PRO LYS GLU ASP VAL ILE SEQRES 13 A 164 ILE GLU SER VAL THR VAL SER GLU HELIX 1 1 ALA A 20 GLY A 34 1 15 HELIX 2 2 GLU A 71 GLY A 75 5 5 HELIX 3 3 ASN A 105 ASN A 109 5 5 HELIX 4 4 GLY A 129 LYS A 137 1 9 SHEET 1 A 9 THR A 39 ILE A 40 0 SHEET 2 A 9 ILE A 156 VAL A 162 -1 O ILE A 157 N THR A 39 SHEET 3 A 9 VAL A 2 THR A 6 -1 N THR A 3 O THR A 161 SHEET 4 A 9 GLY A 9 THR A 15 -1 O ILE A 11 N PHE A 4 SHEET 5 A 9 ALA A 124 ASP A 128 -1 O VAL A 127 N VAL A 12 SHEET 6 A 9 THR A 82 ALA A 86 -1 N LEU A 83 O ALA A 124 SHEET 7 A 9 GLN A 97 ASN A 101 -1 O ASN A 101 N THR A 82 SHEET 8 A 9 ILE A 50 GLY A 52 -1 N GLY A 52 O PHE A 98 SHEET 9 A 9 ARG A 43 VAL A 44 -1 N ARG A 43 O GLN A 51 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