PDB Short entry for 1JBI HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 05-JUN-01 1JBI TITLE NMR STRUCTURE OF THE LCCL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: COCHLIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LCCL MODULE; COMPND 5 SYNONYM: COCH-5B2; COMPND 6 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: M13MP18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM 109; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMED23 KEYWDS ALPHA-BETA PROTEIN, STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.LIEPINSH,M.TREXLER,A.KAIKKONEN,J.WEIGELT,L.BANYAI,L.PATTHY,G.OTTING REVDAT 3 23-FEB-22 1JBI 1 REMARK SEQADV REVDAT 2 24-FEB-09 1JBI 1 VERSN REVDAT 1 17-OCT-01 1JBI 0 JRNL AUTH E.LIEPINSH,M.TREXLER,A.KAIKKONEN,J.WEIGELT,L.BANYAI, JRNL AUTH 2 L.PATTHY,G.OTTING JRNL TITL NMR STRUCTURE OF THE LCCL DOMAIN AND IMPLICATIONS FOR DFNA9 JRNL TITL 2 DEAFNESS DISORDER. JRNL REF EMBO J. V. 20 5347 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11574466 JRNL DOI 10.1093/EMBOJ/20.19.5347 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, OPAL 2.2 REMARK 3 AUTHORS : BRUKER (XWINNMR), LUGINBUHL (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2532 RESTRAINTS, 1193 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 270 DIHEDRAL ANGLE RESTRAINTS AND 69 REMARK 3 RESIDUAL DIPOLAR COUPLING RESTRAINTS REMARK 4 REMARK 4 1JBI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013587. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301; 301 REMARK 210 PH : 4.9; 4.9 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM LCCL; 90% H2O, 10% D2O; REMARK 210 3MG/ML LCCL U-15N; 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY,2D ROESY, 2D DQF REMARK 210 -COSY,2D TOCSY; 3D-15N-SEPARATED-NOESY,3D-15N-SEPARATED-TOCSY, REMARK 210 1H-15N-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PROSA 3.4, XEASY 2.6, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY,TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES 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: 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 90 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 5 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 8 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 9 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 14 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 19 TYR A 67 CB - CG - CD1 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 CYS A 8 13.37 54.33 REMARK 500 1 CYS A 28 75.51 41.15 REMARK 500 1 LEU A 30 63.95 -69.52 REMARK 500 1 ILE A 39 -67.02 63.36 REMARK 500 1 SER A 60 -13.00 -145.86 REMARK 500 1 ARG A 90 62.08 61.28 REMARK 500 1 SER A 92 35.50 -78.82 REMARK 500 2 CYS A 8 13.70 51.24 REMARK 500 2 CYS A 28 70.33 41.05 REMARK 500 2 ILE A 39 -64.12 62.03 REMARK 500 2 SER A 60 -14.32 -146.84 REMARK 500 2 ARG A 90 62.28 65.07 REMARK 500 2 SER A 92 33.96 -78.78 REMARK 500 2 ALA A 93 115.35 -165.91 REMARK 500 3 ALA A 2 98.89 -179.99 REMARK 500 3 THR A 7 46.27 -102.21 REMARK 500 3 CYS A 8 13.00 51.21 REMARK 500 3 CYS A 28 70.49 32.35 REMARK 500 3 ILE A 39 -60.84 63.64 REMARK 500 3 SER A 60 -13.46 -147.09 REMARK 500 3 ARG A 90 61.86 60.09 REMARK 500 3 SER A 92 33.79 -78.91 REMARK 500 3 ALA A 93 112.50 -161.92 REMARK 500 4 CYS A 8 13.45 56.51 REMARK 500 4 ALA A 20 147.39 -175.86 REMARK 500 4 CYS A 28 70.76 28.19 REMARK 500 4 ILE A 39 -65.59 61.39 REMARK 500 4 SER A 60 -66.07 -146.86 REMARK 500 4 PRO A 70 -179.35 -68.18 REMARK 500 4 SER A 92 33.81 -80.50 REMARK 500 5 CYS A 8 13.23 51.82 REMARK 500 5 CYS A 28 71.89 40.79 REMARK 500 5 ILE A 39 -66.97 62.44 REMARK 500 5 ASN A 59 73.47 -65.90 REMARK 500 5 SER A 60 -13.80 -147.20 REMARK 500 5 PRO A 70 171.11 -59.70 REMARK 500 5 SER A 89 79.32 -100.47 REMARK 500 5 SER A 92 33.79 -78.91 REMARK 500 5 ALA A 93 108.68 -161.96 REMARK 500 6 CYS A 8 13.68 49.82 REMARK 500 6 ARG A 16 64.42 -119.89 REMARK 500 6 CYS A 28 76.63 42.08 REMARK 500 6 ILE A 39 -61.29 63.90 REMARK 500 6 ASN A 59 74.35 -64.03 REMARK 500 6 SER A 60 -21.27 -146.72 REMARK 500 6 SER A 92 33.39 -78.73 REMARK 500 6 ALA A 93 95.44 -160.27 REMARK 500 7 PRO A 3 -179.79 -64.99 REMARK 500 7 CYS A 8 13.32 57.85 REMARK 500 7 CYS A 28 76.09 40.87 REMARK 500 REMARK 500 THIS ENTRY HAS 158 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 THR A 1 ALA A 2 4 -65.98 REMARK 500 THR A 1 ALA A 2 19 -139.20 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 TYR A 41 0.07 SIDE CHAIN REMARK 500 1 ARG A 65 0.13 SIDE CHAIN REMARK 500 1 TYR A 67 0.08 SIDE CHAIN REMARK 500 2 ARG A 72 0.10 SIDE CHAIN REMARK 500 3 TYR A 36 0.08 SIDE CHAIN REMARK 500 3 ARG A 72 0.12 SIDE CHAIN REMARK 500 5 ARG A 72 0.09 SIDE CHAIN REMARK 500 6 TYR A 41 0.08 SIDE CHAIN REMARK 500 6 TYR A 67 0.07 SIDE CHAIN REMARK 500 6 ARG A 90 0.09 SIDE CHAIN REMARK 500 8 ARG A 54 0.09 SIDE CHAIN REMARK 500 9 ARG A 16 0.09 SIDE CHAIN REMARK 500 9 TYR A 41 0.07 SIDE CHAIN REMARK 500 10 TYR A 41 0.08 SIDE CHAIN REMARK 500 10 TYR A 67 0.07 SIDE CHAIN REMARK 500 11 ARG A 16 0.10 SIDE CHAIN REMARK 500 11 TYR A 41 0.07 SIDE CHAIN REMARK 500 12 TYR A 75 0.08 SIDE CHAIN REMARK 500 12 ARG A 90 0.08 SIDE CHAIN REMARK 500 13 ARG A 90 0.15 SIDE CHAIN REMARK 500 14 ARG A 54 0.15 SIDE CHAIN REMARK 500 14 ARG A 72 0.08 SIDE CHAIN REMARK 500 15 ARG A 16 0.12 SIDE CHAIN REMARK 500 15 ARG A 72 0.11 SIDE CHAIN REMARK 500 16 ARG A 16 0.08 SIDE CHAIN REMARK 500 16 TYR A 41 0.10 SIDE CHAIN REMARK 500 18 ARG A 72 0.10 SIDE CHAIN REMARK 500 19 TYR A 36 0.07 SIDE CHAIN REMARK 500 20 TYR A 41 0.11 SIDE CHAIN REMARK 500 20 ARG A 90 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1JBI A 1 100 UNP O43405 COCH_HUMAN 27 126 SEQADV 1JBI THR A 1 UNP O43405 ALA 27 CONFLICT SEQADV 1JBI LEU A 99 UNP O43405 LYS 125 CONFLICT SEQADV 1JBI GLU A 100 UNP O43405 GLY 126 CONFLICT SEQRES 1 A 100 THR ALA PRO ILE ALA ILE THR CYS PHE THR ARG GLY LEU SEQRES 2 A 100 ASP ILE ARG LYS GLU LYS ALA ASP VAL LEU CYS PRO GLY SEQRES 3 A 100 GLY CYS PRO LEU GLU GLU PHE SER VAL TYR GLY ASN ILE SEQRES 4 A 100 VAL TYR ALA SER VAL SER SER ILE CYS GLY ALA ALA VAL SEQRES 5 A 100 HIS ARG GLY VAL ILE SER ASN SER GLY GLY PRO VAL ARG SEQRES 6 A 100 VAL TYR SER LEU PRO GLY ARG GLU ASN TYR SER SER VAL SEQRES 7 A 100 ASP ALA ASN GLY ILE GLN SER GLN MET LEU SER ARG TRP SEQRES 8 A 100 SER ALA SER PHE THR VAL THR LEU GLU HELIX 1 1 SER A 46 GLY A 55 1 10 SHEET 1 A 5 ILE A 4 ALA A 5 0 SHEET 2 A 5 LYS A 19 CYS A 24 1 O ASP A 21 N ILE A 4 SHEET 3 A 5 GLY A 62 LEU A 69 -1 N GLY A 62 O CYS A 24 SHEET 4 A 5 SER A 94 THR A 98 -1 O SER A 94 N LEU A 69 SHEET 5 A 5 TYR A 41 ALA A 42 -1 N TYR A 41 O PHE A 95 SHEET 1 B 3 VAL A 35 TYR A 36 0 SHEET 2 B 3 GLN A 84 GLN A 86 1 O GLN A 84 N VAL A 35 SHEET 3 B 3 VAL A 78 ASP A 79 -1 O VAL A 78 N SER A 85 SSBOND 1 CYS A 8 CYS A 24 1555 1555 2.04 SSBOND 2 CYS A 28 CYS A 48 1555 1555 2.03 CRYST1 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