HEADER METAL BINDING PROTEIN 18-OCT-23 8WTH TITLE CRYSTAL STRUCTURE OF CAS3-HD COMPND MOL_ID: 1; COMPND 2 MOLECULE: HD CAS3-TYPE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII OT3; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 GENE: PH0916; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAS3-HD IS A DI-ION DEPENDENT SSDNA NUCLEASE, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.MO REVDAT 2 16-OCT-24 8WTH 1 REMARK REVDAT 1 24-JUL-24 8WTH 0 JRNL AUTH X.MO JRNL TITL STRUCTURAL INSIGHT INTO DYNAMIC CHARACTERISTIC OF THE JRNL TITL 2 POLYMERIZED FORMS OF KINETOPLASTID MEMBRANE PROTEIN-11 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 2996 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.262 REMARK 3 R VALUE (WORKING SET) : 0.261 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 143 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 25.8000 - 3.4500 1.00 2853 143 0.2607 0.2946 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.409 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.685 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.69 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 : 0.003 1567 REMARK 3 ANGLE : 0.686 2108 REMARK 3 CHIRALITY : 0.043 231 REMARK 3 PLANARITY : 0.005 265 REMARK 3 DIHEDRAL : 5.281 204 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 8WTH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300041981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2998 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.450 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.57 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG8000, 0. 2 M AMMONIUM SULFATE, REMARK 280 AND 0.1 M TRIS AT A PH OF 6.4, EVAPORATION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.32800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.85300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.32800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.85300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 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 ARG A 116 REMARK 465 GLU A 117 REMARK 465 LYS A 118 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 GLU A 8 -23.72 71.24 REMARK 500 ASN A 9 -71.60 -128.27 REMARK 500 LYS A 10 1.83 -150.14 REMARK 500 TYR A 31 -61.37 -101.66 REMARK 500 HIS A 111 23.46 -140.36 REMARK 500 ASN A 152 -10.97 69.94 REMARK 500 TRP A 153 -11.84 65.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 8WTH A 3 190 UNP O58617 O58617_PYRHO 3 190 SEQADV 8WTH MET A 2 UNP O58617 INITIATING METHIONINE SEQRES 1 A 189 MET VAL CYS THR PHE PHE GLU ASN LYS VAL CYS VAL GLU SEQRES 2 A 189 THR MET GLU ASP HIS ILE ARG LYS GLY LEU GLU ILE ILE SEQRES 3 A 189 GLU GLY LEU TYR LEU ARG ARG GLY TYR GLY HIS PHE LEU SEQRES 4 A 189 SER LYS ILE LEU ASN ILE ASP VAL LYS LEU ALA GLU GLU SEQRES 5 A 189 LEU LEU LYS LYS ALA TYR ILE PHE HIS ASP ILE GLY LYS SEQRES 6 A 189 CYS LEU GLU GLU PHE GLN GLN ARG ARG GLU LYS PHE ARG SEQRES 7 A 189 PHE HIS GLU VAL TYR SER ALA LEU VAL ALA ARG GLU VAL SEQRES 8 A 189 PHE LYS LYS TYR GLY ASP ILE GLY GLY VAL VAL SER VAL SEQRES 9 A 189 ALA ILE LEU LEU HIS HIS HIS ASN TRP ILE ARG GLU LYS SEQRES 10 A 189 SER PRO LYS ARG PRO ARG ASN LEU LYS LEU CYS ASN GLU SEQRES 11 A 189 CYS LEU SER ILE ILE LYS LYS LEU SER GLY GLU LYS ILE SEQRES 12 A 189 PRO GLU GLU ILE PRO TRP ARG ASN TRP ILE GLU PHE THR SEQRES 13 A 189 GLU GLU ALA GLU GLU ILE MET ARG THR ASN LEU ARG GLY SEQRES 14 A 189 VAL TYR SER ILE LEU LEU PRO LEU VAL VAL ALA ASP ASN SEQRES 15 A 189 TYR ALA ALA ALA VAL ASN ARG HELIX 1 AA1 MET A 16 LEU A 30 1 15 HELIX 2 AA2 TYR A 31 ARG A 34 5 4 HELIX 3 AA3 GLY A 35 LEU A 44 1 10 HELIX 4 AA4 ASP A 47 PHE A 61 1 15 HELIX 5 AA5 HIS A 62 CYS A 67 5 6 HELIX 6 AA6 LEU A 68 ARG A 75 1 8 HELIX 7 AA7 PHE A 80 PHE A 93 1 14 HELIX 8 AA8 LYS A 94 TYR A 96 5 3 HELIX 9 AA9 GLY A 97 LEU A 109 1 13 HELIX 10 AB1 CYS A 129 SER A 140 1 12 HELIX 11 AB2 TRP A 153 ASN A 167 1 15 HELIX 12 AB3 ASN A 167 ARG A 190 1 24 SHEET 1 AA1 2 CYS A 4 PHE A 6 0 SHEET 2 AA1 2 GLU A 14 THR A 15 -1 O GLU A 14 N THR A 5 SSBOND 1 CYS A 4 CYS A 12 1555 1555 2.03 SSBOND 2 CYS A 67 CYS A 132 1555 1555 2.02 CRYST1 112.656 41.706 47.983 90.00 98.88 90.00 C 1 2 1 4 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 0.008877 0.000000 0.001387 0.00000 SCALE2 0.000000 0.023977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021094 0.00000