HEADER DNA BINDING PROTEIN 05-APR-16 5J6X TITLE CRYSTAL STRUCTURE OF THE APO-ZALPHA OF ZEBRAFISH PKZ COMPND MOL_ID: 1; COMPND 2 MOLECULE: Z-DNA BINDING PROTEIN KINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-69; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: PKZ; 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_VARIANT: DE3 KEYWDS PKZ ZDNA ZALPHA WHTH, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.K.SUBRAMANI,D.KIM,K.K.KIM REVDAT 3 08-NOV-23 5J6X 1 REMARK REVDAT 2 15-SEP-21 5J6X 1 JRNL REMARK REVDAT 1 07-SEP-16 5J6X 0 JRNL AUTH V.K.SUBRAMANI,D.KIM,K.YUN,K.K.KIM JRNL TITL STRUCTURAL AND FUNCTIONAL STUDIES OF A LARGE WINGED JRNL TITL 2 Z-DNA-BINDING DOMAIN OF DANIO RERIO PROTEIN KINASE PKZ JRNL REF FEBS LETT. V. 590 2275 2016 JRNL REFN ISSN 0014-5793 JRNL PMID 27265117 JRNL DOI 10.1002/1873-3468.12238 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 4802 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.6876 - 3.5933 0.97 1433 168 0.1565 0.2235 REMARK 3 2 3.5933 - 2.8529 1.00 1448 156 0.2035 0.3198 REMARK 3 3 2.8529 - 2.4925 0.99 1440 157 0.2258 0.3391 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1116 REMARK 3 ANGLE : 1.107 1496 REMARK 3 CHIRALITY : 0.042 165 REMARK 3 PLANARITY : 0.005 191 REMARK 3 DIHEDRAL : 17.301 438 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5J6X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2-7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 28.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4KMF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HIGH CONCENTRATION (3MM) OF THE REMARK 280 PURIFIED PROTEIN IN 20 MM HEPES [4-(2-HYDROXYETHYL)-1- REMARK 280 PIPERAZINEETHANESULFONIC ACID], 80 MM SODIUM CHLORIDE WAS STORED REMARK 280 AT 4DEGC. CRYSTALS WERE CRYO-PROTECTED WITH 35% (V/V) PEG400., REMARK 280 PH 7.5, EVAPORATION, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.68450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.84225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.52675 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LYS B 3 REMARK 465 MET B 4 DBREF 5J6X A 1 69 UNP Q5NE12 Q5NE12_DANRE 1 69 DBREF 5J6X B 1 69 UNP Q5NE12 Q5NE12_DANRE 1 69 SEQADV 5J6X GLY A -2 UNP Q5NE12 EXPRESSION TAG SEQADV 5J6X SER A -1 UNP Q5NE12 EXPRESSION TAG SEQADV 5J6X HIS A 0 UNP Q5NE12 EXPRESSION TAG SEQADV 5J6X GLY B -2 UNP Q5NE12 EXPRESSION TAG SEQADV 5J6X SER B -1 UNP Q5NE12 EXPRESSION TAG SEQADV 5J6X HIS B 0 UNP Q5NE12 EXPRESSION TAG SEQRES 1 A 72 GLY SER HIS MET ALA LYS MET SER ALA GLU ASN GLU ILE SEQRES 2 A 72 GLU MET ARG ILE CYS ASP TYR LEU ARG ARG HIS GLY ARG SEQRES 3 A 72 SER THR VAL GLN ASP ILE PHE LYS GLU LEU LYS LEU GLU SEQRES 4 A 72 LYS SER THR VAL ASN ARG HIS LEU TYR SER LEU GLN ALA SEQRES 5 A 72 SER LYS GLN VAL PHE LYS THR VAL GLU ASP ASN LYS ARG SEQRES 6 A 72 PRO VAL TRP ASP LEU VAL GLU SEQRES 1 B 72 GLY SER HIS MET ALA LYS MET SER ALA GLU ASN GLU ILE SEQRES 2 B 72 GLU MET ARG ILE CYS ASP TYR LEU ARG ARG HIS GLY ARG SEQRES 3 B 72 SER THR VAL GLN ASP ILE PHE LYS GLU LEU LYS LEU GLU SEQRES 4 B 72 LYS SER THR VAL ASN ARG HIS LEU TYR SER LEU GLN ALA SEQRES 5 B 72 SER LYS GLN VAL PHE LYS THR VAL GLU ASP ASN LYS ARG SEQRES 6 B 72 PRO VAL TRP ASP LEU VAL GLU FORMUL 3 HOH *17(H2 O) HELIX 1 AA1 SER A 5 GLY A 22 1 18 HELIX 2 AA2 THR A 25 LEU A 33 1 9 HELIX 3 AA3 GLU A 36 SER A 50 1 15 HELIX 4 AA4 ALA B 6 GLY B 22 1 17 HELIX 5 AA5 THR B 25 LYS B 34 1 10 HELIX 6 AA6 GLU B 36 SER B 50 1 15 SHEET 1 AA1 2 VAL A 53 THR A 56 0 SHEET 2 AA1 2 VAL A 64 LEU A 67 -1 O VAL A 64 N THR A 56 SHEET 1 AA2 2 VAL B 53 THR B 56 0 SHEET 2 AA2 2 VAL B 64 LEU B 67 -1 O VAL B 64 N THR B 56 CRYST1 44.304 44.304 71.369 90.00 90.00 90.00 P 41 8 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 0.022571 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014012 0.00000