PDB Short entry for 1X62 HEADER STRUCTURAL PROTEIN 17-MAY-05 1X62 TITLE SOLUTION STRUCTURE OF THE LIM DOMAIN OF CARBOXYL TERMINAL LIM DOMAIN TITLE 2 PROTEIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TERMINAL LIM DOMAIN PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIM DOMAIN; COMPND 5 SYNONYM: LIM DOMAIN PROTEIN CLP-36, ELFIN; 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: PDLIM1, CLIM1, CLP36; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040830-06; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS LIM DOMAIN, PDZ AND LIM DOMAIN PROTEIN 1, LIM DOMAIN PROTEIN CLP-36, KEYWDS 2 C-TERMINAL LIM DOMAIN PROTEIN 1, CONTRACTILE PROTEIN, STRUCTURAL KEYWDS 3 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 4 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 5 INITIATIVE, RSGI, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.R.QIN,T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 02-MAR-22 1X62 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1X62 1 VERSN REVDAT 1 17-NOV-05 1X62 0 JRNL AUTH X.R.QIN,T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE LIM DOMAIN OF CARBOXYL TERMINAL JRNL TITL 2 LIM DOMAIN PROTEIN 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT,P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X62 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024424. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.18MM 13C,15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL(PH7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3, REMARK 210 0.01MM ZNCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9296, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SPECTROMETER_ID 1 FOR 3D_15N_SEPARATED_NOESY; REMARK 210 SPECTROMETER_ID 2 FOR 3D_13C_SEPARATED_NOESY 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: 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 PRO A 16 91.70 -69.76 REMARK 500 1 ARG A 33 -72.04 -31.97 REMARK 500 1 CYS A 47 -63.34 -93.83 REMARK 500 1 GLU A 66 -36.89 -33.41 REMARK 500 1 PRO A 76 -179.32 -69.75 REMARK 500 2 ARG A 33 -76.06 -32.10 REMARK 500 2 TYR A 42 6.18 -69.85 REMARK 500 2 ASN A 50 107.64 -55.22 REMARK 500 2 GLN A 53 -60.81 -97.54 REMARK 500 2 PRO A 76 2.78 -69.75 REMARK 500 3 ARG A 33 -72.70 -32.05 REMARK 500 3 TYR A 42 -19.09 -45.26 REMARK 500 3 GLN A 53 -65.39 -92.81 REMARK 500 3 VAL A 73 -25.11 -39.96 REMARK 500 4 PRO A 16 95.02 -69.77 REMARK 500 4 ARG A 33 -72.68 -32.01 REMARK 500 4 CYS A 47 -63.87 -92.62 REMARK 500 4 GLU A 66 -39.75 -33.97 REMARK 500 5 PRO A 16 91.23 -69.77 REMARK 500 5 ARG A 33 -74.24 -32.61 REMARK 500 5 CYS A 47 -60.81 -91.52 REMARK 500 6 LYS A 20 -70.43 -66.08 REMARK 500 6 ARG A 33 -74.49 -31.99 REMARK 500 6 CYS A 47 -60.44 -90.17 REMARK 500 6 ASN A 50 108.74 -57.15 REMARK 500 6 PRO A 76 -178.15 -69.72 REMARK 500 7 ARG A 33 -73.68 -32.26 REMARK 500 7 CYS A 47 -63.88 -95.94 REMARK 500 7 ASN A 50 109.90 -58.97 REMARK 500 8 CYS A 21 -69.06 -94.43 REMARK 500 8 ARG A 33 -74.15 -32.44 REMARK 500 8 CYS A 47 -62.44 -94.26 REMARK 500 9 PRO A 16 92.50 -69.78 REMARK 500 9 ARG A 33 -73.59 -32.01 REMARK 500 9 CYS A 47 -64.13 -92.70 REMARK 500 9 GLN A 53 -61.52 -94.66 REMARK 500 10 ARG A 33 -75.26 -32.02 REMARK 500 10 PRO A 76 11.66 -69.73 REMARK 500 11 PRO A 16 97.30 -69.76 REMARK 500 11 ARG A 33 -76.04 -32.01 REMARK 500 12 CYS A 21 -67.35 -97.59 REMARK 500 12 ARG A 33 -73.44 -32.00 REMARK 500 12 CYS A 47 -62.38 -93.68 REMARK 500 12 ASN A 50 109.19 -58.60 REMARK 500 13 ARG A 33 -73.79 -33.30 REMARK 500 14 PRO A 16 94.16 -69.76 REMARK 500 14 ARG A 33 -73.48 -32.02 REMARK 500 14 CYS A 47 -64.42 -92.56 REMARK 500 14 GLU A 66 -39.79 -32.71 REMARK 500 15 ASP A 34 28.89 32.66 REMARK 500 REMARK 500 THIS ENTRY HAS 73 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 CYS A 21 SG 93.6 REMARK 620 3 HIS A 38 ND1 104.9 108.3 REMARK 620 4 CYS A 41 SG 105.8 116.7 122.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 44 SG REMARK 620 2 CYS A 47 SG 105.3 REMARK 620 3 CYS A 65 SG 104.5 107.3 REMARK 620 4 HIS A 68 ND1 128.0 103.9 106.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002002948.1 RELATED DB: TARGETDB DBREF 1X62 A 8 73 UNP O00151 PDLI1_HUMAN 249 314 SEQADV 1X62 GLY A 1 UNP O00151 CLONING ARTIFACT SEQADV 1X62 SER A 2 UNP O00151 CLONING ARTIFACT SEQADV 1X62 SER A 3 UNP O00151 CLONING ARTIFACT SEQADV 1X62 GLY A 4 UNP O00151 CLONING ARTIFACT SEQADV 1X62 SER A 5 UNP O00151 CLONING ARTIFACT SEQADV 1X62 SER A 6 UNP O00151 CLONING ARTIFACT SEQADV 1X62 GLY A 7 UNP O00151 CLONING ARTIFACT SEQADV 1X62 SER A 74 UNP O00151 CLONING ARTIFACT SEQADV 1X62 GLY A 75 UNP O00151 CLONING ARTIFACT SEQADV 1X62 PRO A 76 UNP O00151 CLONING ARTIFACT SEQADV 1X62 SER A 77 UNP O00151 CLONING ARTIFACT SEQADV 1X62 SER A 78 UNP O00151 CLONING ARTIFACT SEQADV 1X62 GLY A 79 UNP O00151 CLONING ARTIFACT SEQRES 1 A 79 GLY SER SER GLY SER SER GLY SER ILE GLY ASN ALA GLN SEQRES 2 A 79 LYS LEU PRO MET CYS ASP LYS CYS GLY THR GLY ILE VAL SEQRES 3 A 79 GLY VAL PHE VAL LYS LEU ARG ASP ARG HIS ARG HIS PRO SEQRES 4 A 79 GLU CYS TYR VAL CYS THR ASP CYS GLY THR ASN LEU LYS SEQRES 5 A 79 GLN LYS GLY HIS PHE PHE VAL GLU ASP GLN ILE TYR CYS SEQRES 6 A 79 GLU LYS HIS ALA ARG GLU ARG VAL SER GLY PRO SER SER SEQRES 7 A 79 GLY HET ZN A 201 1 HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ASN A 50 GLY A 55 1 6 HELIX 2 2 CYS A 65 SER A 74 1 10 SHEET 1 A 2 VAL A 30 LYS A 31 0 SHEET 2 A 2 HIS A 36 ARG A 37 -1 O ARG A 37 N VAL A 30 SHEET 1 B 2 PHE A 57 PHE A 58 0 SHEET 2 B 2 ILE A 63 TYR A 64 -1 O TYR A 64 N PHE A 57 LINK SG CYS A 18 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 21 ZN ZN A 201 1555 1555 2.32 LINK ND1 HIS A 38 ZN ZN A 201 1555 1555 2.08 LINK SG CYS A 41 ZN ZN A 201 1555 1555 2.38 LINK SG CYS A 44 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 47 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 65 ZN ZN A 401 1555 1555 2.33 LINK ND1 HIS A 68 ZN ZN A 401 1555 1555 2.03 SITE 1 AC1 4 CYS A 18 CYS A 21 HIS A 38 CYS A 41 SITE 1 AC2 5 CYS A 44 ASP A 46 CYS A 47 CYS A 65 SITE 2 AC2 5 HIS A 68 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