PDB Short entry for 4A24 HEADER TRANSCRIPTION 22-SEP-11 4A24 TITLE STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE DEAF-1 AND BS69 MYND DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 501-544; COMPND 5 SYNONYM: DEAF-1 MYND, NUCLEAR DEAF-1-RELATED TRANSCRIPTIONAL COMPND 6 REGULATOR SUPPRESSIN, ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 5; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PETMTHX(MODIFIED FROM PET24D); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETMTHX-MYND KEYWDS TRANSCRIPTION, ZINC-BINDING, TRANSCRIPTIONAL REGULATION, PROTEIN KEYWDS 2 BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.KATEB,H.PERRIN,K.TRIPSIANES,P.ZOU,R.SPADACCINI,M.BOTTOMLEY, AUTHOR 2 A.BEPPERLING,S.ANSIEAU,M.SATTLER REVDAT 4 14-JUN-23 4A24 1 REMARK LINK ATOM REVDAT 3 24-JAN-18 4A24 1 REMARK REVDAT 2 13-FEB-13 4A24 1 JRNL REVDAT 1 07-NOV-12 4A24 0 JRNL AUTH F.KATEB,H.PERRIN,K.TRIPSIANES,P.ZOU,R.SPADACCINI, JRNL AUTH 2 M.BOTTOMLEY,T.M.FRANZMANN,J.BUCHNER,S.ANSIEAU,M.SATTLER JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE DEAF-1 AND BS69 JRNL TITL 2 MYND DOMAINS. JRNL REF PLOS ONE V. 8 54715 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23372760 JRNL DOI 10.1371/JOURNAL.PONE.0054715 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS-ARIA REMARK 3 AUTHORS : NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE RESTRAINTS DERIVED FROM THE REMARK 3 CYANA CALCULATIONS, TORSION ANGLE RESTRAINTS DERIVED FROM TALOS REMARK 3 BASED ON SECONDARY CHEMICAL SHIFTS, AND RDC RESTRAINTS WERE REMARK 3 APPLIED FOR A WATER REFINEMENT CALCULATION USING A SIMULATED REMARK 3 ANNEALING PROTOCOL IN CNS. THE ZINC COORDINATION GEOMETRY WAS REMARK 3 DEFINED AND MAINTAINED BY DISTANCE AND ANGLE CONSTRAINTS. . REMARK 4 REMARK 4 4A24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1290049655. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295.0; 295.0; 295.0; 295.0 REMARK 210 PH : 6.5; 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 100; 100; 100; 100 REMARK 210 PRESSURE : 1.0 ATM; 1.0 ATM; 1.0 ATM; 1.0 REMARK 210 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY (ALIPHATIC REMARK 210 CARBONS); 3D 1H- 13C NOESY REMARK 210 (AROMATIC CARBONS) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, TALOS, SPARKY, CYANA, REMARK 210 ARIA-CNS 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 : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE CHEMICAL SHIFTS OF THE DEAF-1 MYND DOMAIN WERE REMARK 210 ASSIGNED USING STANDARD HETERONUCLEAR EXPERIMENTS ACQUIRED AT REMARK 210 295 K ON A 1 MM UNIFORMLY 15N,13C LABELED SAMPLE. EXPERIMENTS REMARK 210 WERE CARRIED OUT ON BRUKER SPECTROMETERS OPERATING AT A PROTON REMARK 210 FREQUENCY BETWEEN 500 AND 900 MHZ. ALL SPECTRA WERE PROCESSED REMARK 210 USING THE PACKAGE NMRPIPE- NMRDRAW 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 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 HIS A 536 H CYS A 540 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 MET A 500 -38.80 -140.15 REMARK 500 1 CYS A 507 -87.32 -122.47 REMARK 500 1 ARG A 509 -9.86 -53.46 REMARK 500 1 MET A 512 -24.40 -148.26 REMARK 500 1 GLN A 542 -79.73 -73.88 REMARK 500 1 SER A 543 60.81 89.78 REMARK 500 2 ALA A 499 28.13 -141.76 REMARK 500 2 CYS A 507 -73.60 -121.29 REMARK 500 2 ARG A 509 -9.24 -52.57 REMARK 500 2 ALA A 511 153.19 -46.05 REMARK 500 2 MET A 512 -29.09 -168.11 REMARK 500 3 ALA A 499 138.63 66.70 REMARK 500 3 CYS A 507 -75.10 -123.53 REMARK 500 3 ARG A 509 -7.69 -54.59 REMARK 500 3 GLU A 510 -0.93 -58.65 REMARK 500 3 ALA A 511 152.56 -46.54 REMARK 500 3 MET A 512 -28.23 -160.03 REMARK 500 4 CYS A 507 -83.31 -122.44 REMARK 500 4 ARG A 509 -8.14 -52.23 REMARK 500 4 MET A 512 -24.49 -163.29 REMARK 500 5 CYS A 507 -82.49 -122.23 REMARK 500 5 ARG A 509 -8.44 -55.22 REMARK 500 6 ALA A 499 -64.25 -108.63 REMARK 500 6 MET A 500 33.55 -148.69 REMARK 500 6 CYS A 507 -83.85 -121.56 REMARK 500 7 ALA A 499 -78.87 -164.67 REMARK 500 7 CYS A 507 -70.84 -120.70 REMARK 500 7 ARG A 509 -7.87 -50.20 REMARK 500 7 MET A 512 -27.49 -166.90 REMARK 500 8 CYS A 507 -75.08 -127.12 REMARK 500 8 ARG A 509 -9.97 -53.80 REMARK 500 8 GLU A 510 0.62 -61.87 REMARK 500 8 ALA A 511 163.79 -46.49 REMARK 500 8 MET A 512 -28.21 -178.44 REMARK 500 8 TYR A 523 -169.14 -126.20 REMARK 500 9 ALA A 499 -9.04 -157.84 REMARK 500 9 MET A 500 -25.07 -157.38 REMARK 500 9 CYS A 507 -86.06 -128.99 REMARK 500 10 ALA A 499 -174.26 65.76 REMARK 500 10 CYS A 507 -82.29 -120.53 REMARK 500 10 GLU A 510 3.94 -66.36 REMARK 500 10 MET A 512 -29.67 -173.45 REMARK 500 10 SER A 543 98.37 -60.59 REMARK 500 11 MET A 500 -11.98 -150.97 REMARK 500 11 MET A 512 -27.86 -153.92 REMARK 500 11 GLN A 542 -79.97 66.58 REMARK 500 12 MET A 500 18.75 -151.45 REMARK 500 12 CYS A 507 -86.35 -122.69 REMARK 500 13 CYS A 507 -83.92 -122.03 REMARK 500 13 ARG A 509 -7.81 -53.48 REMARK 500 REMARK 500 THIS ENTRY HAS 77 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 504 SG REMARK 620 2 CYS A 507 SG 111.2 REMARK 620 3 CYS A 524 SG 112.0 109.9 REMARK 620 4 CYS A 528 SG 109.7 107.3 106.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 515 SG REMARK 620 2 CYS A 518 SG 111.7 REMARK 620 3 HIS A 536 NE2 108.2 107.8 REMARK 620 4 CYS A 540 SG 108.1 110.0 111.1 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18004 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FIRST THREE RESIDUES, GAM, RESULT FROM THE TEV REMARK 999 CLEAVAGE SITE TO REMOVE THE N-TERMINAL TAG DBREF 4A24 A 501 544 UNP O75398 DEAF1_HUMAN 501 544 SEQADV 4A24 GLY A 498 UNP O75398 EXPRESSION TAG SEQADV 4A24 ALA A 499 UNP O75398 EXPRESSION TAG SEQADV 4A24 MET A 500 UNP O75398 EXPRESSION TAG SEQRES 1 A 47 GLY ALA MET GLU GLN SER CYS VAL ASN CYS GLY ARG GLU SEQRES 2 A 47 ALA MET SER GLU CYS THR GLY CYS HIS LYS VAL ASN TYR SEQRES 3 A 47 CYS SER THR PHE CYS GLN ARG LYS ASP TRP LYS ASP HIS SEQRES 4 A 47 GLN HIS ILE CYS GLY GLN SER ALA HET ZN A 601 1 HET ZN A 602 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 SER A 525 ASP A 532 1 8 HELIX 2 2 ASP A 532 CYS A 540 1 9 SHEET 1 AA 2 SER A 513 GLU A 514 0 SHEET 2 AA 2 ASN A 522 TYR A 523 -1 N TYR A 523 O SER A 513 LINK SG CYS A 504 ZN ZN A 601 1555 1555 2.31 LINK SG CYS A 507 ZN ZN A 601 1555 1555 2.28 LINK SG CYS A 515 ZN ZN A 602 1555 1555 2.31 LINK SG CYS A 518 ZN ZN A 602 1555 1555 2.31 LINK SG CYS A 524 ZN ZN A 601 1555 1555 2.28 LINK SG CYS A 528 ZN ZN A 601 1555 1555 2.27 LINK NE2 HIS A 536 ZN ZN A 602 1555 1555 1.97 LINK SG CYS A 540 ZN ZN A 602 1555 1555 2.31 SITE 1 AC1 4 CYS A 504 CYS A 507 CYS A 524 CYS A 528 SITE 1 AC2 4 CYS A 515 CYS A 518 HIS A 536 CYS A 540 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