HEADER TRANSCRIPTION 26-FEB-11 2L9Z TITLE ZINC KNUCKLE IN PRDM4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PR DOMAIN ZINC FINGER PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 366-402; COMPND 5 SYNONYM: PR DOMAIN-CONTAINING PROTEIN 4; 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: PRDM4, PFM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-4T1 KEYWDS ZINC-BINDING DOMAIN, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.BRIKNAROVA,D.Z.ATWATER,J.M.GLICKEN,S.J.MAYNARD,T.E.NESS REVDAT 4 01-MAY-24 2L9Z 1 REMARK SEQADV LINK REVDAT 3 29-JUN-11 2L9Z 1 JRNL REVDAT 2 11-MAY-11 2L9Z 1 JRNL REVDAT 1 27-APR-11 2L9Z 0 JRNL AUTH K.BRIKNAROVA,D.Z.ATWATER,J.M.GLICKEN,S.J.MAYNARD,T.E.NESS JRNL TITL THE PR/SET DOMAIN IN PRDM4 IS PRECEDED BY A ZINC KNUCKLE. JRNL REF PROTEINS V. 79 2341 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 21604305 JRNL DOI 10.1002/PROT.23057 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, ARIA 2.3 REMARK 3 AUTHORS : VARIAN (VNMRJ), LINGE, O'DONOGHUE AND NILGES REMARK 3 (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000102142. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.1-7.2 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM PRDM4(366-402), 2.5 MM REMARK 210 ZINC ION, 50 MM D11-TRIS, 2.5 MM REMARK 210 D16-TCEP, 90% H2O/10% D2O; 0.5 REMARK 210 MM PRDM4(366-402), 2.5 MM ZINC REMARK 210 ION, 50 MM D11-TRIS, 2.5 MM D16- REMARK 210 TCEP, 100% D2O; 0.25 MM [U-100% REMARK 210 15N] PRDM4(366-402), 1.6 MM ZINC REMARK 210 ION, 50 MM D11-TRIS, 2.5 MM D16- REMARK 210 TCEP, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY; ECOSY; 2D 1H-15N REMARK 210 HSQC; 3D HNHA; 3D HNHB; 3D 1H- REMARK 210 15N TOCSY; 3D 1H-15N NOESY; 2D REMARK 210 1H-15N HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNIFORM NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, ARIA 2.3 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 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 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 SER A 365 27.93 -153.68 REMARK 500 1 MET A 369 -81.54 65.78 REMARK 500 1 SER A 386 -158.28 -154.03 REMARK 500 1 PRO A 398 44.59 -77.14 REMARK 500 2 GLU A 367 -72.34 73.08 REMARK 500 2 HIS A 391 -49.04 -141.70 REMARK 500 3 SER A 365 175.23 65.87 REMARK 500 3 LYS A 366 31.77 -147.91 REMARK 500 3 THR A 374 -67.91 -106.42 REMARK 500 4 SER A 365 70.64 57.50 REMARK 500 4 LYS A 366 -71.39 -61.50 REMARK 500 4 PHE A 373 78.95 57.33 REMARK 500 4 PRO A 393 63.49 -69.97 REMARK 500 4 PHE A 396 -167.54 46.61 REMARK 500 5 LYS A 366 41.22 -148.86 REMARK 500 5 SER A 386 -165.33 -169.11 REMARK 500 5 PRO A 393 80.35 -69.95 REMARK 500 5 ASP A 399 -92.46 59.52 REMARK 500 6 SER A 365 40.61 -102.83 REMARK 500 6 THR A 371 75.99 48.74 REMARK 500 6 SER A 386 -156.50 -138.66 REMARK 500 6 VAL A 394 78.05 57.51 REMARK 500 6 PRO A 401 46.78 -73.93 REMARK 500 7 MET A 369 -80.41 67.17 REMARK 500 7 PHE A 373 -162.81 -118.53 REMARK 500 7 THR A 374 -79.36 -78.75 REMARK 500 7 SER A 386 -166.74 -122.27 REMARK 500 7 THR A 395 38.15 -142.43 REMARK 500 7 PHE A 396 107.85 68.20 REMARK 500 7 THR A 400 94.62 66.92 REMARK 500 7 PRO A 401 84.32 -67.51 REMARK 500 8 LYS A 366 169.82 69.15 REMARK 500 8 LEU A 372 -64.00 70.05 REMARK 500 8 SER A 386 -159.11 -116.41 REMARK 500 9 ALA A 370 106.15 -54.19 REMARK 500 9 PHE A 373 -165.58 58.83 REMARK 500 9 THR A 374 -58.19 -142.71 REMARK 500 9 SER A 386 -168.11 -167.24 REMARK 500 9 PRO A 393 103.29 -53.74 REMARK 500 9 PRO A 401 92.21 -64.95 REMARK 500 10 GLU A 367 96.51 65.07 REMARK 500 10 THR A 371 94.21 52.16 REMARK 500 10 PRO A 389 30.49 -73.58 REMARK 500 10 GLU A 390 -51.28 -162.78 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 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 CYS A 380 SG 111.8 REMARK 620 3 CYS A 388 SG 111.9 109.4 REMARK 620 4 HIS A 391 ND1 107.2 108.2 108.2 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 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17494 RELATED DB: BMRB DBREF 2L9Z A 366 402 UNP Q9UKN5 PRDM4_HUMAN 366 402 SEQADV 2L9Z GLY A 364 UNP Q9UKN5 EXPRESSION TAG SEQADV 2L9Z SER A 365 UNP Q9UKN5 EXPRESSION TAG SEQRES 1 A 39 GLY SER LYS GLU ASN MET ALA THR LEU PHE THR ILE TRP SEQRES 2 A 39 CYS THR LEU CYS ASP ARG ALA TYR PRO SER ASP CYS PRO SEQRES 3 A 39 GLU HIS GLY PRO VAL THR PHE VAL PRO ASP THR PRO ILE HET ZN A 403 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 THR A 378 ASP A 381 5 4 SHEET 1 A 2 ILE A 375 CYS A 377 0 SHEET 2 A 2 ARG A 382 TYR A 384 -1 O ARG A 382 N CYS A 377 LINK SG CYS A 377 ZN ZN A 403 1555 1555 2.30 LINK SG CYS A 380 ZN ZN A 403 1555 1555 2.30 LINK SG CYS A 388 ZN ZN A 403 1555 1555 2.30 LINK ND1 HIS A 391 ZN ZN A 403 1555 1555 2.00 SITE 1 AC1 4 CYS A 377 CYS A 380 CYS A 388 HIS A 391 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