HEADER SIGNALING PROTEIN 19-SEP-18 6MIF TITLE LIM5 DOMAIN OF PINCH1 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIM AND SENESCENT CELL ANTIGEN-LIKE-CONTAINING DOMAIN COMPND 3 PROTEIN 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN 1,PINCH-1,RENAL COMPND 6 CARCINOMA ANTIGEN NY-REN-48; COMPND 7 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: LIMS1, PINCH, PINCH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS LIM DOMAIN, ZN BINDING, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.QIN,J.VAYNBERG REVDAT 4 14-JUN-23 6MIF 1 LINK REVDAT 3 20-MAY-20 6MIF 1 JRNL REVDAT 2 04-DEC-19 6MIF 1 REMARK REVDAT 1 31-OCT-18 6MIF 0 JRNL AUTH J.VAYNBERG,K.FUKUDA,F.LU,K.BIALKOWSKA,Y.CHEN,E.F.PLOW,J.QIN JRNL TITL NON-CATALYTIC SIGNALING BY PSEUDOKINASE ILK FOR REGULATING JRNL TITL 2 CELL ADHESION. JRNL REF NAT COMMUN V. 9 4465 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30367047 JRNL DOI 10.1038/S41467-018-06906-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000237003. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20MM NACL REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-15N] LIM5-T, 90% REMARK 210 H2O/10% D2O; 1.0 MM [U-13C; U- REMARK 210 15N] 15N 13C LIM5-T, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HNCACB; 3D HNHA; 3D REMARK 210 C(CO)NH; 3D 1H-15N NOESY; 3D 1H- REMARK 210 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 : NMRPIPE, PIPP, XWINNMR, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 O LEU A 318 H LEU A 322 1.46 REMARK 500 H PHE A 294 O LYS A 297 1.58 REMARK 500 O CYS A 252 H ASN A 256 1.58 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 252 102.80 -49.78 REMARK 500 1 SER A 265 104.97 -55.45 REMARK 500 1 CYS A 278 102.96 -39.76 REMARK 500 1 CYS A 281 -4.77 -140.12 REMARK 500 2 CYS A 252 101.03 -48.04 REMARK 500 2 SER A 265 103.48 -58.07 REMARK 500 2 ASN A 268 -0.58 70.87 REMARK 500 2 CYS A 278 102.54 -40.39 REMARK 500 2 CYS A 281 -2.48 -144.84 REMARK 500 2 ASN A 282 11.85 59.79 REMARK 500 3 CYS A 252 101.94 -48.73 REMARK 500 3 SER A 265 103.64 -58.05 REMARK 500 3 ASN A 268 -0.78 71.97 REMARK 500 3 CYS A 278 105.61 -41.70 REMARK 500 3 PHE A 291 -165.46 -103.01 REMARK 500 4 CYS A 252 101.25 -49.02 REMARK 500 4 CYS A 278 105.55 -45.25 REMARK 500 4 CYS A 281 6.14 -152.55 REMARK 500 4 LEU A 322 -83.87 -69.78 REMARK 500 4 ARG A 324 83.52 -69.79 REMARK 500 5 SER A 248 -77.35 65.18 REMARK 500 5 CYS A 252 100.98 -48.90 REMARK 500 5 ASN A 268 -6.80 76.53 REMARK 500 5 CYS A 278 105.71 -42.72 REMARK 500 5 PHE A 291 -164.42 -102.45 REMARK 500 6 CYS A 252 101.64 -48.08 REMARK 500 6 CYS A 278 106.36 -42.65 REMARK 500 6 PHE A 291 -167.02 -103.49 REMARK 500 7 CYS A 252 101.84 -48.55 REMARK 500 7 SER A 265 103.41 -58.80 REMARK 500 7 ASN A 268 -5.01 72.81 REMARK 500 7 CYS A 278 107.17 -43.62 REMARK 500 7 CYS A 281 6.69 -153.71 REMARK 500 7 LEU A 322 -83.86 -75.10 REMARK 500 8 CYS A 252 102.90 -49.38 REMARK 500 8 ASN A 268 -0.41 71.49 REMARK 500 8 CYS A 278 103.33 -39.18 REMARK 500 8 CYS A 281 -3.15 -142.73 REMARK 500 8 PHE A 291 -167.59 -104.17 REMARK 500 9 SER A 248 -165.01 58.69 REMARK 500 9 CYS A 252 100.84 -48.40 REMARK 500 9 SER A 265 105.73 -57.03 REMARK 500 9 CYS A 278 106.40 -41.61 REMARK 500 9 PHE A 291 -166.50 -103.01 REMARK 500 9 ARG A 324 155.42 67.49 REMARK 500 10 CYS A 252 101.86 -48.69 REMARK 500 10 SER A 265 102.94 -57.04 REMARK 500 10 CYS A 278 109.69 -42.25 REMARK 500 10 ARG A 324 134.76 65.19 REMARK 500 11 CYS A 252 101.97 -49.11 REMARK 500 REMARK 500 THIS ENTRY HAS 97 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 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 252 SG REMARK 620 2 CYS A 255 SG 101.0 REMARK 620 3 CYS A 272 SG 102.2 117.8 REMARK 620 4 CYS A 275 SG 112.6 109.3 113.0 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 278 SG REMARK 620 2 CYS A 281 SG 115.8 REMARK 620 3 CYS A 300 SG 108.4 111.0 REMARK 620 4 CYS A 303 SG 120.2 94.8 105.7 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30518 RELATED DB: BMRB REMARK 900 LIM5 DOMAIN OF PINCH1 PROTEIN DBREF 6MIF A 249 325 UNP P48059 LIMS1_HUMAN 249 325 SEQADV 6MIF GLY A 247 UNP P48059 EXPRESSION TAG SEQADV 6MIF SER A 248 UNP P48059 EXPRESSION TAG SEQRES 1 A 79 GLY SER GLY ASP VAL CYS PHE HIS CYS ASN ARG VAL ILE SEQRES 2 A 79 GLU GLY ASP VAL VAL SER ALA LEU ASN LYS ALA TRP CYS SEQRES 3 A 79 VAL ASN CYS PHE ALA CYS SER THR CYS ASN THR LYS LEU SEQRES 4 A 79 THR LEU LYS ASN LYS PHE VAL GLU PHE ASP MET LYS PRO SEQRES 5 A 79 VAL CYS LYS LYS CYS TYR GLU LYS PHE PRO LEU GLU LEU SEQRES 6 A 79 LYS LYS ARG LEU LYS LYS LEU ALA GLU THR LEU GLY ARG SEQRES 7 A 79 LYS HET ZN A 401 1 HET ZN A 402 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 LYS A 301 PHE A 307 1 7 HELIX 2 AA2 PRO A 308 GLU A 320 1 13 SHEET 1 AA1 2 PHE A 291 PHE A 294 0 SHEET 2 AA1 2 LYS A 297 CYS A 300 -1 O LYS A 297 N PHE A 294 LINK SG CYS A 252 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 255 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 272 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 275 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 278 ZN ZN A 401 1555 1555 2.31 LINK SG CYS A 281 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 300 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 303 ZN ZN A 401 1555 1555 2.30 SITE 1 AC1 5 CYS A 278 THR A 280 CYS A 281 CYS A 300 SITE 2 AC1 5 CYS A 303 SITE 1 AC2 4 CYS A 252 CYS A 255 CYS A 272 CYS A 275 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