HEADER TRANSFERASE 30-DEC-08 2KCW TITLE SOLUTION STRUCTURE OF APO-FORM YJAB FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED ACETYLTRANSFERASE YJAB; COMPND 3 CHAIN: A; COMPND 4 EC: 2.3.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YJAB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS GNAT FOLD, ACYLTRANSFERASE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR J.LU,X.WANG,C.JIN REVDAT 4 26-FEB-20 2KCW 1 REMARK REVDAT 3 13-JUL-11 2KCW 1 VERSN REVDAT 2 09-JUN-09 2KCW 1 JRNL REVDAT 1 05-MAY-09 2KCW 0 JRNL AUTH J.LU,X.WANG,B.XIA,C.JIN JRNL TITL SOLUTION STRUCTURE OF APO-YJAB FROM ESCHERICHIA COLI JRNL REF PROTEINS V. 76 261 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 19343803 JRNL DOI 10.1002/PROT.22407 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.1, AMBER 7 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CASE, DARDEN, CHEATHAM, III, SIMMERLING, REMARK 3 WANG, DUKE, LUO AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100963. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 130 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 30MM TRIS, 100MM SODIUM REMARK 210 CHLORIDE, 10MM DTT, 1 MM [U-13C; REMARK 210 U-15N] YJAB PROTEIN, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5, XWINNMR 3.5, CYANA REMARK 210 2.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 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 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 1 GLY A 146 N GLY A 146 CA 0.111 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 9 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 ARG A 22 NH1 - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -7.9 DEGREES REMARK 500 1 TYR A 35 CB - CG - CD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 ARG A 44 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 ARG A 59 CG - CD - NE ANGL. DEV. = -12.7 DEGREES REMARK 500 1 ARG A 59 NH1 - CZ - NH2 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 ARG A 59 NE - CZ - NH2 ANGL. DEV. = -9.2 DEGREES REMARK 500 1 MET A 66 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 1 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 ARG A 89 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 ARG A 127 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 1 ARG A 127 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 TYR A 144 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 VAL A 145 CA - C - O ANGL. DEV. = -19.3 DEGREES REMARK 500 1 VAL A 145 O - C - N ANGL. DEV. = 12.3 DEGREES REMARK 500 1 GLY A 146 C - N - CA ANGL. DEV. = 29.1 DEGREES REMARK 500 1 GLY A 146 N - CA - C ANGL. DEV. = 19.0 DEGREES REMARK 500 1 GLY A 146 CA - C - N ANGL. DEV. = -16.7 DEGREES REMARK 500 1 ALA A 147 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 6 ARG A 44 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 8 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 ARG A 127 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 14 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 17 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 21 ARG A 127 NE - CZ - NH2 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 46 -56.29 -140.09 REMARK 500 1 ASP A 132 -47.88 -161.16 REMARK 500 2 PHE A 46 -56.45 -135.24 REMARK 500 2 ASP A 132 -46.52 -161.81 REMARK 500 2 PRO A 136 43.94 -78.11 REMARK 500 3 PHE A 46 -56.77 -136.09 REMARK 500 3 ASP A 131 -73.39 -73.45 REMARK 500 3 ASP A 132 -40.82 -165.04 REMARK 500 3 PRO A 136 42.38 -64.73 REMARK 500 4 PHE A 46 -56.28 -136.06 REMARK 500 4 ASN A 110 69.51 -105.71 REMARK 500 4 ASP A 132 -38.45 -160.40 REMARK 500 5 PHE A 46 -54.86 -137.40 REMARK 500 5 PRO A 51 45.51 -80.17 REMARK 500 5 ASP A 132 -37.43 -161.07 REMARK 500 5 PRO A 136 71.05 -60.43 REMARK 500 5 PRO A 138 143.99 -36.22 REMARK 500 6 PHE A 46 -59.64 -138.12 REMARK 500 6 ASP A 132 -49.26 -157.17 REMARK 500 6 LEU A 133 32.60 -90.18 REMARK 500 6 PRO A 136 46.09 -78.09 REMARK 500 6 PRO A 138 147.20 -34.26 REMARK 500 7 PHE A 46 -52.59 -136.89 REMARK 500 7 PRO A 51 43.74 -80.43 REMARK 500 7 ASP A 132 -45.61 -161.73 REMARK 500 7 PRO A 136 45.62 -78.04 REMARK 500 8 LEU A 31 99.54 -67.09 REMARK 500 8 PHE A 46 -53.98 -136.98 REMARK 500 8 PRO A 51 46.27 -80.17 REMARK 500 8 ASP A 132 -39.73 -163.48 REMARK 500 8 PRO A 136 63.17 -64.97 REMARK 500 9 PHE A 46 -55.86 -136.39 REMARK 500 9 ASP A 132 -52.10 -159.54 REMARK 500 10 PHE A 46 -59.21 -137.96 REMARK 500 10 ASP A 131 -65.41 -91.28 REMARK 500 10 ASP A 132 -43.15 -157.15 REMARK 500 11 LEU A 31 97.84 -66.01 REMARK 500 11 PHE A 46 -52.70 -136.29 REMARK 500 11 ASP A 132 -45.91 -163.65 REMARK 500 11 PRO A 136 60.41 -63.74 REMARK 500 12 LEU A 31 97.21 -64.21 REMARK 500 12 PHE A 46 -56.13 -137.40 REMARK 500 12 PRO A 51 47.90 -80.46 REMARK 500 12 ASP A 132 -47.94 -159.08 REMARK 500 12 LEU A 133 33.44 -90.66 REMARK 500 12 PRO A 136 46.25 -78.35 REMARK 500 13 PHE A 46 -55.32 -136.79 REMARK 500 13 PRO A 51 48.85 -80.65 REMARK 500 13 ASP A 132 -45.54 -165.05 REMARK 500 14 PHE A 46 -56.43 -136.38 REMARK 500 REMARK 500 THIS ENTRY HAS 81 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 GLY A 146 ALA A 147 1 125.99 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 1 HIS A 10 0.09 SIDE CHAIN REMARK 500 1 TYR A 35 0.12 SIDE CHAIN REMARK 500 1 TYR A 144 0.18 SIDE CHAIN REMARK 500 10 ARG A 22 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 GLY A 146 21.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16098 RELATED DB: BMRB DBREF 2KCW A 1 147 UNP P09163 YJAB_ECOLI 1 147 SEQRES 1 A 147 MET VAL ILE SER ILE ARG ARG SER ARG HIS GLU GLU GLY SEQRES 2 A 147 GLU GLU LEU VAL ALA ILE TRP CYS ARG SER VAL ASP ALA SEQRES 3 A 147 THR HIS ASP PHE LEU SER ALA GLU TYR ARG THR GLU LEU SEQRES 4 A 147 GLU ASP LEU VAL ARG SER PHE LEU PRO GLU ALA PRO LEU SEQRES 5 A 147 TRP VAL ALA VAL ASN GLU ARG ASP GLN PRO VAL GLY PHE SEQRES 6 A 147 MET LEU LEU SER GLY GLN HIS MET ASP ALA LEU PHE ILE SEQRES 7 A 147 ASP PRO ASP VAL ARG GLY CYS GLY VAL GLY ARG VAL LEU SEQRES 8 A 147 VAL GLU HIS ALA LEU SER MET ALA PRO GLU LEU THR THR SEQRES 9 A 147 ASN VAL ASN GLU GLN ASN GLU GLN ALA VAL GLY PHE TYR SEQRES 10 A 147 LYS LYS VAL GLY PHE LYS VAL THR GLY ARG SER GLU VAL SEQRES 11 A 147 ASP ASP LEU GLY LYS PRO TYR PRO LEU LEU ASN LEU ALA SEQRES 12 A 147 TYR VAL GLY ALA HELIX 1 1 GLU A 12 HIS A 28 1 17 HELIX 2 2 SER A 32 SER A 45 1 14 HELIX 3 3 ASP A 79 GLY A 84 1 6 HELIX 4 4 GLY A 86 ALA A 99 1 14 HELIX 5 5 ASN A 110 GLY A 121 1 12 SHEET 1 A 7 ILE A 3 ARG A 7 0 SHEET 2 A 7 TRP A 53 ASN A 57 -1 O VAL A 54 N ARG A 6 SHEET 3 A 7 PRO A 62 SER A 69 -1 O VAL A 63 N ALA A 55 SHEET 4 A 7 HIS A 72 ILE A 78 -1 O PHE A 77 N PHE A 65 SHEET 5 A 7 THR A 103 ASN A 107 1 O THR A 103 N MET A 73 SHEET 6 A 7 LEU A 139 TYR A 144 -1 O LEU A 142 N THR A 104 SHEET 7 A 7 PHE A 122 ARG A 127 -1 N LYS A 123 O ALA A 143 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