HEADER METAL BINDING PROTEIN 08-JAN-03 1J2O TITLE STRUCTURE OF FLIN2, A COMPLEX CONTAINING THE N-TERMINAL LIM DOMAIN OF TITLE 2 LMO2 AND LDB1-LID COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUSION OF RHOMBOTIN-2 AND LIM DOMAIN-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FLIN2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: PROTEIN IS A FUSION OF THE N-TERMINAL LIM DOMAIN OF COMPND 7 LMO2 (RESIDUES 26-87) FOLLOWED BY AN ELEVEN RESIDUE LINKER COMPND 8 (GGSGGHMGSGG) THAN THE LID DOMAIN FROM LDB1 (RESIDUES 300-339). COMPND 9 ORIGINALLY EXPRESSED AS A FUSION WITH GST. GST PORTION REMOVED BY COMPND 10 TREATMENT WITH THROMBIN. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: LMO2, LDB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS LIM DOMAIN, LIM-INTERACTION-DOMAIN (LID), METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.E.DEANE,J.P.MACKAY,A.H.KWAN,E.Y.SUM,J.E.VISVADER,J.M.MATTHEWS REVDAT 6 27-DEC-23 1J2O 1 REMARK REVDAT 5 23-FEB-22 1J2O 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 1J2O 1 VERSN REVDAT 3 30-DEC-03 1J2O 1 AUTHOR REVDAT 2 23-DEC-03 1J2O 1 SEQADV REVDAT 1 13-MAY-03 1J2O 0 JRNL AUTH J.E.DEANE,J.P.MACKAY,A.H.KWAN,E.Y.SUM,J.E.VISVADER, JRNL AUTH 2 J.M.MATTHEWS JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF LDB1 BY THE JRNL TITL 2 N-TERMINAL LIM DOMAINS OF LMO2 AND LMO4 JRNL REF EMBO J. V. 22 2224 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12727888 JRNL DOI 10.1093/EMBOJ/CDG196 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.E.DEANE,J.E.VISVADER,J.P.MACKAY,J.M.MATTHEWS REMARK 1 TITL DESIGN, PRODUCTION AND CHARACTERIZATION OF FLIN2 AND FLIN4: REMARK 1 TITL 2 THE ENGINEERING OF INTRAMOLECULAR LDB1:LMO COMPLEXES. REMARK 1 REF PROTEIN ENG. V. 14 493 2001 REMARK 1 REFN ISSN 0269-2139 REMARK 1 DOI 10.1093/PROTEIN/14.7.493 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, CNS 1.1 REMARK 3 AUTHORS : GUNTERT ET AL. (DYANA), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 1690 NOE REMARK 3 CONTRAINTS (INCLUDING 50 AMBIGUOUS CONSTRAINTS) AND 134 TORSION REMARK 3 ANGLE RESTAINTS REMARK 4 REMARK 4 1J2O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000005554. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : FLIN2 0.5MM, NACL 50MM, DTRIS REMARK 210 -HCL 20MM, PH 7.0, REMARK 210 DITHIOTHREITOL 1MM, TSP; REMARK 210 UNIFORMLY 15-N LABELLED FLIN2 REMARK 210 0.5MM, NACL 50MM, DTRIS-HCL 20MM, REMARK 210 PH 7.0, DITHIOTHREITOL 1MM, DSS; REMARK 210 UNIFORMLY 13-C/15-N LABELLED REMARK 210 0.5MM, NACL 50MM, NAH2P04/ REMARK 210 NA2HPO4 20MM, PH 7.0, REMARK 210 DITHIOTHREITOL 1MM, DSS REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.5, XEASY 1.3.13, REMARK 210 TALOS, ARIA 1.1.2, CNS 1.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 AUTOMATED NOE ASSIGNMENT OF REMARK 210 AMBIGUOUS NOES REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: BACKBONE AND SIDE-CHAIN ASSIGNMENT MADE USING STANDARD 2D REMARK 210 AND 3D EXPERIMENTS. 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 H GLY A 74 HA LEU A 84 1.19 REMARK 500 HB2 LEU A 40 H GLY A 41 1.35 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 ASN A 12 145.36 77.22 REMARK 500 1 ALA A 21 -43.36 179.21 REMARK 500 1 ASP A 23 -12.19 176.50 REMARK 500 1 CYS A 38 -118.22 -110.68 REMARK 500 1 ARG A 39 43.66 -170.83 REMARK 500 1 LEU A 40 -112.70 43.01 REMARK 500 1 ARG A 45 -93.08 -158.97 REMARK 500 1 ARG A 46 -169.85 -104.12 REMARK 500 1 LEU A 51 -50.00 -29.59 REMARK 500 1 THR A 83 -96.50 53.11 REMARK 500 1 LEU A 84 95.93 -51.08 REMARK 500 1 MET A 85 -47.25 -140.47 REMARK 500 1 PHE A 89 -153.49 -59.54 REMARK 500 1 ASP A 91 -109.00 -122.65 REMARK 500 1 GLU A 92 -44.92 76.85 REMARK 500 1 GLU A 94 -163.49 -78.03 REMARK 500 1 ARG A 95 73.78 -67.75 REMARK 500 1 ASP A 106 -68.39 -4.16 REMARK 500 1 ALA A 107 64.02 72.32 REMARK 500 1 ILE A 111 43.18 -94.64 REMARK 500 2 ASN A 12 128.66 71.65 REMARK 500 2 ALA A 21 -47.87 170.48 REMARK 500 2 ASP A 23 -22.30 178.97 REMARK 500 2 CYS A 38 -90.38 -78.02 REMARK 500 2 GLU A 42 -107.56 49.63 REMARK 500 2 ARG A 62 -86.44 -164.08 REMARK 500 2 HIS A 69 -91.65 -124.80 REMARK 500 2 ASP A 91 -84.31 -86.91 REMARK 500 2 GLU A 92 -45.41 67.57 REMARK 500 2 THR A 103 -104.91 -115.21 REMARK 500 2 GLN A 104 93.51 -168.19 REMARK 500 2 PHE A 105 -57.71 -129.65 REMARK 500 2 ILE A 111 -101.88 -98.19 REMARK 500 3 LEU A 3 -66.56 -102.43 REMARK 500 3 ASN A 12 134.49 71.88 REMARK 500 3 ALA A 21 -53.24 178.22 REMARK 500 3 ASP A 23 -12.58 178.82 REMARK 500 3 CYS A 38 -98.52 -112.51 REMARK 500 3 GLU A 42 -91.58 58.58 REMARK 500 3 SER A 66 43.46 28.95 REMARK 500 3 PRO A 82 -144.81 -88.79 REMARK 500 3 ASP A 91 -112.62 -93.42 REMARK 500 3 GLU A 92 -67.31 -168.10 REMARK 500 3 ASP A 93 -34.83 -140.73 REMARK 500 3 GLU A 94 106.37 73.90 REMARK 500 3 ARG A 95 -145.42 -92.18 REMARK 500 3 LEU A 96 -139.31 -155.62 REMARK 500 3 THR A 103 -96.54 -83.78 REMARK 500 3 GLN A 104 86.63 -168.33 REMARK 500 3 ASP A 106 -56.50 -124.99 REMARK 500 REMARK 500 THIS ENTRY HAS 402 RAMACHANDRAN OUTLIERS. 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 16 ARG A 45 -11.42 REMARK 500 17 TYR A 48 10.03 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 115 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 107.9 REMARK 620 3 HIS A 27 ND1 110.1 108.8 REMARK 620 4 CYS A 30 SG 110.1 109.9 110.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 116 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 33 SG REMARK 620 2 CYS A 36 SG 114.9 REMARK 620 3 CYS A 56 SG 116.8 119.6 REMARK 620 4 ASP A 59 OD1 108.6 59.7 125.0 REMARK 620 5 ASP A 59 OD2 99.8 100.1 99.9 41.2 REMARK 620 N 1 2 3 4 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 115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 116 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M3V RELATED DB: PDB REMARK 900 1M3V CONTAINS SIMILAR PROTEIN DBREF 1J2O A 2 63 UNP P25801 RHM2_MOUSE 26 87 DBREF 1J2O A 75 114 UNP P70662 LDB1_MOUSE 300 339 SEQADV 1J2O GLY A 1 UNP P25801 CLONING ARTIFACT SEQADV 1J2O GLY A 64 UNP P25801 LINKER SEQADV 1J2O GLY A 65 UNP P25801 LINKER SEQADV 1J2O SER A 66 UNP P25801 LINKER SEQADV 1J2O GLY A 67 UNP P25801 LINKER SEQADV 1J2O GLY A 68 UNP P25801 LINKER SEQADV 1J2O HIS A 69 UNP P25801 LINKER SEQADV 1J2O MET A 70 UNP P25801 LINKER SEQADV 1J2O GLY A 71 UNP P25801 LINKER SEQADV 1J2O SER A 72 UNP P25801 LINKER SEQADV 1J2O GLY A 73 UNP P25801 LINKER SEQADV 1J2O GLY A 74 UNP P25801 LINKER SEQRES 1 A 114 GLY SER LEU LEU THR CYS GLY GLY CYS GLN GLN ASN ILE SEQRES 2 A 114 GLY ASP ARG TYR PHE LEU LYS ALA ILE ASP GLN TYR TRP SEQRES 3 A 114 HIS GLU ASP CYS LEU SER CYS ASP LEU CYS GLY CYS ARG SEQRES 4 A 114 LEU GLY GLU VAL GLY ARG ARG LEU TYR TYR LYS LEU GLY SEQRES 5 A 114 ARG LYS LEU CYS ARG ARG ASP TYR LEU ARG LEU GLY GLY SEQRES 6 A 114 SER GLY GLY HIS MET GLY SER GLY GLY ASP VAL MET VAL SEQRES 7 A 114 VAL GLY GLU PRO THR LEU MET GLY GLY GLU PHE GLY ASP SEQRES 8 A 114 GLU ASP GLU ARG LEU ILE THR ARG LEU GLU ASN THR GLN SEQRES 9 A 114 PHE ASP ALA ALA ASN GLY ILE ASP ASP GLU HET ZN A 115 1 HET ZN A 116 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 CYS A 56 GLY A 64 1 9 SHEET 1 A 3 TYR A 25 TRP A 26 0 SHEET 2 A 3 TYR A 17 LYS A 20 -1 N LEU A 19 O TRP A 26 SHEET 3 A 3 THR A 98 GLU A 101 -1 O LEU A 100 N PHE A 18 LINK SG CYS A 6 ZN ZN A 115 1555 1555 2.28 LINK SG CYS A 9 ZN ZN A 115 1555 1555 2.27 LINK ND1 HIS A 27 ZN ZN A 115 1555 1555 2.00 LINK SG CYS A 30 ZN ZN A 115 1555 1555 2.31 LINK SG CYS A 33 ZN ZN A 116 1555 1555 2.25 LINK SG CYS A 36 ZN ZN A 116 1555 1555 2.24 LINK SG CYS A 56 ZN ZN A 116 1555 1555 2.28 LINK OD1 ASP A 59 ZN ZN A 116 1555 1555 3.28 LINK OD2 ASP A 59 ZN ZN A 116 1555 1555 2.02 SITE 1 AC1 4 CYS A 6 CYS A 9 HIS A 27 CYS A 30 SITE 1 AC2 4 CYS A 33 CYS A 36 CYS A 56 ASP A 59 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