HEADER HYDROLASE, METAL BINDING PROTEIN 22-OCT-10 2L4Z TITLE NMR STRUCTURE OF FUSION OF CTIP (641-685) TO LMO4-LIM1 (18-82) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA ENDONUCLEASE RBBP8,LIM DOMAIN TRANSCRIPTION FACTOR COMPND 3 LMO4; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: CTBP-INTERACTING PROTEIN,CTIP,RETINOBLASTOMA-BINDING PROTEIN COMPND 6 8,RBBP-8,RETINOBLASTOMA-INTERACTING PROTEIN AND MYOSIN-LIKE,RIM, COMPND 7 SPORULATION IN THE ABSENCE OF SPO11 PROTEIN 2 HOMOLOG,SAE2,BREAST COMPND 8 TUMOR AUTOANTIGEN,LIM DOMAIN ONLY PROTEIN 4,LMO-4; COMPND 9 EC: 3.1.-.-; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 OTHER_DETAILS: THE FUSION PROTEIN OF CTIP (UNP 641-685), LINKER (901- COMPND 13 911) AND LMO4 (UNP 18-82) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HUMAN, MOUSE; SOURCE 4 ORGANISM_TAXID: 9606, 10090; SOURCE 5 GENE: RBBP8, CTIP, LMO4; 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: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX-2T KEYWDS LIM DOMAIN, PROTEIN-PROTEIN INTERACTION, LIM-INTERACTION DOMAIN, KEYWDS 2 LMO4, RBBP8/CTIP, LIM-ONLY PROTEIN, HYDROLASE, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.LIEW,P.H.STOKES,A.H.KWAN,J.M.MATTHEWS REVDAT 4 26-JUL-23 2L4Z 1 SOURCE REMARK DBREF SEQADV REVDAT 4 2 1 LINK REVDAT 3 01-JAN-20 2L4Z 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV REVDAT 2 27-MAR-13 2L4Z 1 JRNL REVDAT 1 26-OCT-11 2L4Z 0 JRNL AUTH P.H.STOKES,C.W.LIEW,A.H.KWAN,P.FOO,H.E.BARKER,A.DJAMIRZE, JRNL AUTH 2 V.O'REILLY,J.E.VISVADER,J.P.MACKAY,J.M.MATTHEWS JRNL TITL STRUCTURAL BASIS OF THE INTERACTION OF THE BREAST CANCER JRNL TITL 2 ONCOGENE LMO4 WITH THE TUMOUR SUPPRESSOR CTIP/RBBP8. JRNL REF J.MOL.BIOL. V. 425 1101 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23353824 JRNL DOI 10.1016/J.JMB.2013.01.017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.1-2.1, ARIA 1.2 REMARK 3 AUTHORS : BRUKER (TOPSPIN), LINGE, O'DONOGHUE AND NILGES REMARK 3 (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000101963. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 291; 281; 303 REMARK 210 PH : 6; 6; 6 REMARK 210 IONIC STRENGTH : 150; 150; 150 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 150 UM [U-15N] FUSION PROTEIN-1, REMARK 210 20 MM SODIUM PHOSPHATE-2, 150 MM REMARK 210 SODIUM CHLORIDE-3, 1 MM DTT-4, REMARK 210 90% H2O/10% D2O; 500 UM [U-99% REMARK 210 13C; U-99% 15N] FUSION PROTEIN-5, REMARK 210 20 MM SODIUM PHOSPHATE-6, 150 REMARK 210 MM SODIUM CHLORIDE-7, 1 MM DTT-8, REMARK 210 90% H2O/10% D2O; 300 UM [U-99% REMARK 210 13C; U-99% 15N] FUSION PROTEIN-9, REMARK 210 20 MM SODIUM PHOSPHATE-10, 150 REMARK 210 MM SODIUM CHLORIDE-11, 1 MM DTT- REMARK 210 12, 100% D2O; 500 UM FUSION REMARK 210 PROTEIN-13, 20 MM SODIUM REMARK 210 PHOSPHATE-14, 150 MM SODIUM REMARK 210 CHLORIDE-15, 1 MM DTT-16, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HNCO; 3D 1H-15N REMARK 210 NOESY; 3D HNHA; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D CCH-TOCSY; 3D 1H- REMARK 210 13C NOESY; 2D 1H-1H NOESY; 2D 1H- REMARK 210 1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.114, ARIA 1.2, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 639 REMARK 465 SER A 640 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 HD21 LEU A 57 HG SER A 64 1.34 REMARK 500 HZ3 LYS A 67 O GLY A 82 1.59 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 645 100.03 -172.42 REMARK 500 1 SER A 649 49.07 -149.40 REMARK 500 1 PHE A 650 -99.67 -162.00 REMARK 500 1 ILE A 653 54.71 -116.82 REMARK 500 1 LEU A 663 31.65 -95.04 REMARK 500 1 TRP A 20 -114.49 58.81 REMARK 500 1 MET A 39 -72.56 69.50 REMARK 500 1 ASP A 40 -2.10 -166.13 REMARK 500 1 GLN A 56 102.14 -54.95 REMARK 500 1 LYS A 67 -63.89 -166.19 REMARK 500 1 PHE A 81 -91.03 -107.13 REMARK 500 2 SER A 656 85.63 -67.52 REMARK 500 2 LEU A 663 59.43 -90.63 REMARK 500 2 GLN A 680 141.55 -174.11 REMARK 500 2 TRP A 20 -124.01 54.21 REMARK 500 2 ALA A 38 -84.18 -119.55 REMARK 500 2 ASP A 40 -15.53 -178.59 REMARK 500 2 GLN A 56 88.25 -63.70 REMARK 500 2 LYS A 67 -67.28 -158.20 REMARK 500 2 SER A 68 38.67 -91.45 REMARK 500 2 PHE A 81 -95.33 -114.18 REMARK 500 3 GLN A 646 -142.42 -108.01 REMARK 500 3 ILE A 653 56.84 -104.26 REMARK 500 3 ILE A 657 -157.91 -93.26 REMARK 500 3 MET A 907 63.32 -101.29 REMARK 500 3 TRP A 20 -112.15 54.29 REMARK 500 3 ARG A 33 -70.72 -88.85 REMARK 500 3 MET A 39 -64.23 72.68 REMARK 500 3 ASP A 40 -18.95 -165.34 REMARK 500 3 ASP A 59 70.64 -100.66 REMARK 500 3 ILE A 60 -102.91 -124.91 REMARK 500 3 LYS A 67 -42.46 -164.51 REMARK 500 3 PHE A 81 -100.52 -114.89 REMARK 500 4 GLN A 646 38.64 -140.39 REMARK 500 4 ILE A 653 47.64 -102.90 REMARK 500 4 GLN A 654 53.39 -100.58 REMARK 500 4 GLN A 680 49.53 -87.10 REMARK 500 4 LEU A 18 -158.39 -96.48 REMARK 500 4 TRP A 20 -111.06 56.05 REMARK 500 4 ARG A 33 -63.70 72.60 REMARK 500 4 ALA A 38 -110.37 -107.40 REMARK 500 4 ASP A 40 -16.98 74.59 REMARK 500 4 GLN A 56 97.95 -65.05 REMARK 500 4 LYS A 67 -60.18 -166.66 REMARK 500 4 PHE A 81 -64.09 -107.82 REMARK 500 5 LEU A 642 95.23 -55.07 REMARK 500 5 GLN A 643 -61.66 179.16 REMARK 500 5 GLN A 654 49.46 -108.21 REMARK 500 5 TRP A 655 -155.78 -89.70 REMARK 500 5 LEU A 663 50.04 -93.07 REMARK 500 REMARK 500 THIS ENTRY HAS 217 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 110.8 REMARK 620 3 HIS A 44 NE2 106.5 111.7 REMARK 620 4 CYS A 47 SG 110.4 112.7 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 50 SG REMARK 620 2 CYS A 53 SG 114.7 REMARK 620 3 CYS A 73 SG 115.0 113.5 REMARK 620 4 ASP A 76 OD2 104.1 102.0 105.6 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M3V RELATED DB: PDB REMARK 900 RELATED ID: 1RUT RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS FUSION PROTEIN HAS NON-SEQUENTIAL RESIDUE NUMBERING. THE REMARK 999 RESIDUE 901 LINKS TO THE RESIDUE 685 AND THE RESIDUE 18 LINKS TO REMARK 999 THE RESIDUE 911, RESPECTIVELY. DBREF 2L4Z A 641 685 UNP Q99708 CTIP_HUMAN 641 685 DBREF 2L4Z A 18 82 UNP P61969 LMO4_MOUSE 18 82 SEQADV 2L4Z GLY A 639 UNP Q99708 EXPRESSION TAG SEQADV 2L4Z SER A 640 UNP Q99708 EXPRESSION TAG SEQADV 2L4Z GLY A 901 UNP Q99708 LINKER SEQADV 2L4Z GLY A 902 UNP Q99708 LINKER SEQADV 2L4Z SER A 903 UNP Q99708 LINKER SEQADV 2L4Z GLY A 904 UNP Q99708 LINKER SEQADV 2L4Z GLY A 905 UNP Q99708 LINKER SEQADV 2L4Z HIS A 906 UNP Q99708 LINKER SEQADV 2L4Z MET A 907 UNP Q99708 LINKER SEQADV 2L4Z GLY A 908 UNP Q99708 LINKER SEQADV 2L4Z SER A 909 UNP Q99708 LINKER SEQADV 2L4Z GLY A 910 UNP Q99708 LINKER SEQADV 2L4Z GLY A 911 UNP Q99708 LINKER SEQADV 2L4Z SER A 52 UNP P61969 CYS 52 ENGINEERED MUTATION SEQADV 2L4Z SER A 64 UNP P61969 CYS 64 ENGINEERED MUTATION SEQRES 1 A 123 GLY SER SER LEU GLN ASN ASN GLN ASP VAL SER PHE GLU SEQRES 2 A 123 ASN ILE GLN TRP SER ILE ASP PRO GLY ALA ASP LEU SER SEQRES 3 A 123 GLN TYR LYS MET ASP VAL THR VAL ILE ASP THR LYS ASP SEQRES 4 A 123 GLY SER GLN SER LYS LEU GLY GLY GLY GLY SER GLY GLY SEQRES 5 A 123 HIS MET GLY SER GLY GLY LEU SER TRP LYS ARG CYS ALA SEQRES 6 A 123 GLY CYS GLY GLY LYS ILE ALA ASP ARG PHE LEU LEU TYR SEQRES 7 A 123 ALA MET ASP SER TYR TRP HIS SER ARG CYS LEU LYS CYS SEQRES 8 A 123 SER SER CYS GLN ALA GLN LEU GLY ASP ILE GLY THR SER SEQRES 9 A 123 SER TYR THR LYS SER GLY MET ILE LEU CYS ARG ASN ASP SEQRES 10 A 123 TYR ILE ARG LEU PHE GLY HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 PHE A 650 GLN A 654 5 5 HELIX 2 2 GLN A 56 ILE A 60 5 5 HELIX 3 3 CYS A 73 PHE A 81 1 9 SHEET 1 A 3 VAL A 672 ILE A 673 0 SHEET 2 A 3 LEU A 35 ALA A 38 -1 O LEU A 35 N ILE A 673 SHEET 3 A 3 SER A 41 HIS A 44 -1 O TRP A 43 N LEU A 36 LINK SG CYS A 23 ZN ZN A 101 1555 1555 2.26 LINK SG CYS A 26 ZN ZN A 101 1555 1555 2.28 LINK NE2 HIS A 44 ZN ZN A 101 1555 1555 1.95 LINK SG CYS A 47 ZN ZN A 101 1555 1555 2.26 LINK SG CYS A 50 ZN ZN A 102 1555 1555 2.32 LINK SG CYS A 53 ZN ZN A 102 1555 1555 2.28 LINK SG CYS A 73 ZN ZN A 102 1555 1555 2.32 LINK OD2 ASP A 76 ZN ZN A 102 1555 1555 2.02 SITE 1 AC1 4 CYS A 23 CYS A 26 HIS A 44 CYS A 47 SITE 1 AC2 4 CYS A 50 CYS A 53 CYS A 73 ASP A 76 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