PDB Short entry for 2FI2 HEADER TRANSCRIPTION 27-DEC-05 2FI2 TITLE SOLUTION STRUCTURE OF THE SCAN HOMODIMER FROM MZF-1/ZNF42 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN 42; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SCAN DOMAIN, RESIDUES 37-128; COMPND 5 SYNONYM: MYELOID ZINC FINGER 1, MZF-1, ZINC FINGER AND SCAN DOMAIN COMPND 6 CONTAINING PROTEIN 6; 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: ZNF42, MZF1, ZSCAN6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SG13009[PREP4]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30GB1 KEYWDS SCAN DOMAIN, ZNF-42, MZF-1, HOMODIMER, TRANSCRIPTION FACTOR, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, CENTER FOR KEYWDS 3 EUKARYOTIC STRUCTURAL GENOMICS, CESG, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.F.VOLKMAN,F.C.PETERSON,T.L.SANDER,J.K.WALTNER,CENTER FOR EUKARYOTIC AUTHOR 2 STRUCTURAL GENOMICS (CESG) REVDAT 4 09-MAR-22 2FI2 1 REMARK SEQADV REVDAT 3 24-FEB-09 2FI2 1 VERSN REVDAT 2 02-JAN-07 2FI2 1 JRNL SEQADV DBREF REVDAT 1 17-JAN-06 2FI2 0 JRNL AUTH F.C.PETERSON,P.L.HAYES,J.K.WALTNER,A.K.HEISNER,D.R.JENSEN, JRNL AUTH 2 T.L.SANDER,B.F.VOLKMAN JRNL TITL STRUCTURE OF THE SCAN DOMAIN FROM THE TUMOR SUPPRESSOR JRNL TITL 2 PROTEIN MZF1. JRNL REF J.MOL.BIOL. V. 363 137 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16950398 JRNL DOI 10.1016/J.JMB.2006.07.063 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.3. REMARK 3 AUTHORS : SCHWIETERS, C.D., KUSZEWSKI, J.J., TJANDRA, N., REMARK 3 CLORE, G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 4063 NOE CONSTRAINTS REMARK 3 ( 843 INTRA, 818 SEQUENTIAL, 1029 MEDIUM, 750 INTRAMONOMER LONG REMARK 3 RANGE AND 623 INTERMONOMER NOE CONSTRAINTS) REMARK 3 AND 264 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINTS WERE REMARK 3 ASSIGNED AND VALIDATED IN ONE MONOMER AND THEN DUPLICATED TO REMARK 3 GENERATE A SYMMETRY RELATED CONSTRAINTS IN THE SECOND MONOMER. REMARK 3 CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH REMARK 3 MONOMERS. REMARK 4 REMARK 4 2FI2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035902. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 99 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM ZNF-42 U-15N/13C, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM NACL, 90% REMARK 210 H2O, 10% D2O; 1.7 MM ZNF-42 U- REMARK 210 15N/13C, 1.7 MM UNLABELED ZNF-42, REMARK 210 20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 NACL, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C-SEPARATED_NOESY (AROMATIC); 3D_13C-F1- REMARK 210 FILTERED-13C-F3-SEPARATED_NOESY 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 3.5, NMRPIPE 2004, REMARK 210 SPSCAN 1.1.0, XEASY 1.3, GARANT REMARK 210 2.1, CYANA 2.1 REMARK 210 METHOD USED : AUTOMATED METHODS WERE USED FOR REMARK 210 BACKBONE CHEMICAL SHIFT REMARK 210 ASSIGNMENT AND ITERATIVE NOE REMARK 210 REFINEMENT. FINAL STRUCTURES REMARK 210 WERE OBTAINED BY MOLECULAR REMARK 210 DYNAMICS IN EXPLICIT SOLVENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING REMARK 210 A CRYOGENIC PROBE 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HG SER B 79 OE1 GLU B 81 1.55 REMARK 500 HG SER A 79 OE1 GLU A 81 1.56 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 36 -174.80 -171.14 REMARK 500 1 ARG A 74 77.48 54.51 REMARK 500 1 ARG A 108 82.11 63.64 REMARK 500 1 GLU A 125 75.85 59.69 REMARK 500 1 PRO A 126 96.93 -20.88 REMARK 500 1 ARG B 74 74.06 52.39 REMARK 500 1 ARG B 108 87.58 68.86 REMARK 500 1 GLU B 125 99.75 62.69 REMARK 500 2 ARG A 74 78.73 53.25 REMARK 500 2 GLU A 125 132.32 70.72 REMARK 500 2 ARG B 74 81.06 59.30 REMARK 500 2 ARG B 108 78.41 59.53 REMARK 500 2 GLU B 125 95.51 68.66 REMARK 500 3 ARG A 74 82.51 66.50 REMARK 500 3 ARG A 108 80.54 61.97 REMARK 500 3 ARG A 124 -72.16 -161.02 REMARK 500 3 ARG B 74 76.29 60.76 REMARK 500 3 ARG B 108 80.17 63.27 REMARK 500 3 ARG B 124 -46.83 71.07 REMARK 500 4 ARG A 74 79.31 51.56 REMARK 500 4 ARG A 108 85.55 60.00 REMARK 500 4 ARG A 124 -78.14 65.97 REMARK 500 4 ARG B 74 76.64 53.23 REMARK 500 4 ARG B 108 79.60 57.71 REMARK 500 4 ARG B 124 -166.00 61.84 REMARK 500 5 ARG A 74 85.92 60.16 REMARK 500 5 GLN A 107 -60.03 -104.47 REMARK 500 5 ARG A 108 87.36 68.08 REMARK 500 5 ARG B 74 78.56 51.96 REMARK 500 5 GLN B 107 -61.98 -107.37 REMARK 500 5 ARG B 108 83.27 57.38 REMARK 500 6 SER A 36 -41.94 -161.79 REMARK 500 6 ASP A 37 96.42 65.42 REMARK 500 6 ARG A 74 87.78 48.66 REMARK 500 6 ARG A 108 86.73 65.72 REMARK 500 6 GLU A 125 79.26 66.61 REMARK 500 6 ASP B 37 113.60 63.52 REMARK 500 6 ARG B 74 77.83 55.86 REMARK 500 6 ARG B 108 78.00 54.23 REMARK 500 6 GLU B 125 93.23 65.08 REMARK 500 7 ARG A 74 77.20 60.72 REMARK 500 7 ARG A 108 87.05 64.53 REMARK 500 7 ARG A 123 18.05 -66.65 REMARK 500 7 ARG B 74 80.06 52.65 REMARK 500 7 PRO B 98 -51.51 -29.90 REMARK 500 7 ARG B 108 87.02 65.62 REMARK 500 7 ARG B 123 93.29 -66.47 REMARK 500 7 ARG B 124 -31.47 178.73 REMARK 500 8 ARG A 74 79.32 49.56 REMARK 500 8 ARG A 108 78.62 61.39 REMARK 500 REMARK 500 THIS ENTRY HAS 121 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 7 ARG B 48 0.08 SIDE CHAIN REMARK 500 13 ARG A 44 0.07 SIDE CHAIN REMARK 500 18 ARG B 124 0.09 SIDE CHAIN REMARK 500 19 ARG B 123 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.79132 RELATED DB: TARGETDB DBREF 2FI2 A 37 128 UNP P28698 ZNF42_HUMAN 37 128 DBREF 2FI2 B 37 128 UNP P28698 ZNF42_HUMAN 37 128 SEQADV 2FI2 GLY A 35 UNP P28698 CLONING ARTIFACT SEQADV 2FI2 SER A 36 UNP P28698 CLONING ARTIFACT SEQADV 2FI2 GLY B 35 UNP P28698 CLONING ARTIFACT SEQADV 2FI2 SER B 36 UNP P28698 CLONING ARTIFACT SEQRES 1 A 94 GLY SER ASP PRO GLY PRO GLU ALA ALA ARG LEU ARG PHE SEQRES 2 A 94 ARG CYS PHE HIS TYR GLU GLU ALA THR GLY PRO GLN GLU SEQRES 3 A 94 ALA LEU ALA GLN LEU ARG GLU LEU CYS ARG GLN TRP LEU SEQRES 4 A 94 ARG PRO GLU VAL ARG SER LYS GLU GLN MET LEU GLU LEU SEQRES 5 A 94 LEU VAL LEU GLU GLN PHE LEU GLY ALA LEU PRO PRO GLU SEQRES 6 A 94 ILE GLN ALA ARG VAL GLN GLY GLN ARG PRO GLY SER PRO SEQRES 7 A 94 GLU GLU ALA ALA ALA LEU VAL ASP GLY LEU ARG ARG GLU SEQRES 8 A 94 PRO GLY GLY SEQRES 1 B 94 GLY SER ASP PRO GLY PRO GLU ALA ALA ARG LEU ARG PHE SEQRES 2 B 94 ARG CYS PHE HIS TYR GLU GLU ALA THR GLY PRO GLN GLU SEQRES 3 B 94 ALA LEU ALA GLN LEU ARG GLU LEU CYS ARG GLN TRP LEU SEQRES 4 B 94 ARG PRO GLU VAL ARG SER LYS GLU GLN MET LEU GLU LEU SEQRES 5 B 94 LEU VAL LEU GLU GLN PHE LEU GLY ALA LEU PRO PRO GLU SEQRES 6 B 94 ILE GLN ALA ARG VAL GLN GLY GLN ARG PRO GLY SER PRO SEQRES 7 B 94 GLU GLU ALA ALA ALA LEU VAL ASP GLY LEU ARG ARG GLU SEQRES 8 B 94 PRO GLY GLY HELIX 1 1 GLY A 39 CYS A 49 1 11 HELIX 2 2 GLY A 57 ARG A 74 1 18 HELIX 3 3 SER A 79 ALA A 95 1 17 HELIX 4 4 ILE A 100 ARG A 108 1 9 HELIX 5 5 SER A 111 ARG A 123 1 13 HELIX 6 6 GLY B 39 CYS B 49 1 11 HELIX 7 7 GLY B 57 ARG B 74 1 18 HELIX 8 8 SER B 79 ALA B 95 1 17 HELIX 9 9 ILE B 100 ARG B 108 1 9 HELIX 10 10 SER B 111 ARG B 123 1 13 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