HEADER DNA BINDING PROTEIN 22-JUN-21 7OXD TITLE CRYSTAL STRUCTURE OF SCYTONEMA HOFMANNI TRANSPOSITION PROTEIN TNIQ COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHTNIQ; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCYTONEMA HOFMANNII; SOURCE 3 ORGANISM_TAXID: 34078; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRANSPOSITION PROTEIN, ZINC-FINGER PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.QUERQUES,M.JINEK REVDAT 1 01-DEC-21 7OXD 0 JRNL AUTH I.QUERQUES,M.SCHMITZ,S.OBERLI,C.CHANEZ,M.JINEK JRNL TITL TARGET SITE SELECTION AND REMODELLING BY TYPE V JRNL TITL 2 CRISPR-TRANSPOSON SYSTEMS. JRNL REF NATURE V. 599 497 2021 JRNL REFN ESSN 1476-4687 JRNL PMID 34759315 JRNL DOI 10.1038/S41586-021-04030-Z REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.290 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 45126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 4319 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 43.4000 - 4.0400 1.00 2720 145 0.1786 0.1759 REMARK 3 2 4.0400 - 3.2100 1.00 2712 144 0.1672 0.1685 REMARK 3 3 3.2100 - 2.8000 1.00 2716 150 0.1835 0.1956 REMARK 3 4 2.8000 - 2.5400 1.00 2746 141 0.1888 0.2086 REMARK 3 5 2.5400 - 2.3600 1.00 2705 144 0.1809 0.1552 REMARK 3 6 2.3600 - 2.2200 0.99 2692 136 0.1941 0.2267 REMARK 3 7 2.2200 - 2.1100 0.99 2701 143 0.1806 0.1819 REMARK 3 8 2.1100 - 2.0200 1.00 2735 145 0.1806 0.1629 REMARK 3 9 2.0200 - 1.9400 1.00 2717 148 0.1798 0.1940 REMARK 3 10 1.9400 - 1.8700 0.96 2607 138 0.2156 0.1834 REMARK 3 11 1.8700 - 1.8200 1.00 2694 145 0.1901 0.1770 REMARK 3 12 1.8200 - 1.7600 1.00 2731 148 0.1927 0.2006 REMARK 3 13 1.7600 - 1.7200 1.00 2699 147 0.1797 0.2526 REMARK 3 14 1.7200 - 1.6800 1.00 2742 146 0.1903 0.1696 REMARK 3 15 1.6800 - 1.6400 1.00 2736 143 0.1811 0.2068 REMARK 3 16 1.6400 - 1.6000 1.00 2683 146 0.1739 0.2027 REMARK 3 17 1.6000 - 1.5700 1.00 2730 144 0.1814 0.2380 REMARK 3 18 1.5700 - 1.5400 1.00 2689 141 0.1897 0.2322 REMARK 3 19 1.5400 - 1.5100 1.00 2736 142 0.1984 0.2231 REMARK 3 20 1.5100 - 1.4900 1.00 2745 147 0.2013 0.2409 REMARK 3 21 1.4900 - 1.4600 1.00 2723 136 0.2205 0.2399 REMARK 3 22 1.4600 - 1.4400 1.00 2684 146 0.2182 0.2078 REMARK 3 23 1.4400 - 1.4200 1.00 2737 143 0.2272 0.2743 REMARK 3 24 1.4200 - 1.4000 1.00 2726 146 0.2325 0.2391 REMARK 3 25 1.4000 - 1.3800 1.00 2691 146 0.2363 0.2434 REMARK 3 26 1.3800 - 1.3600 1.00 2764 150 0.2479 0.2912 REMARK 3 27 1.3600 - 1.3500 1.00 2673 141 0.2376 0.2776 REMARK 3 28 1.3500 - 1.3300 1.00 2763 144 0.2595 0.2808 REMARK 3 29 1.3300 - 1.3100 1.00 2695 142 0.2698 0.2610 REMARK 3 30 1.3100 - 1.3000 0.99 2641 142 0.3545 0.3506 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.79 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7OXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-19 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 : SLS REMARK 200 BEAMLINE : X06DA 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85839 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 43.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.04553 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 0.96360 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5 20% PEG 6000 250 REMARK 280 MM SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 280K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.81800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.93750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.81800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.93750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 IN SAME ASYMMETRIC UNIT 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 OD1 ASN A 61 CD PRO A 62 1.74 REMARK 500 ND2 ASN A 61 O HOH A 301 1.82 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 ARG A 155 -70.19 -87.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 535 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 536 DISTANCE = 6.15 ANGSTROMS 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 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 102 SG REMARK 620 2 CYS A 105 SG 113.5 REMARK 620 3 CYS A 124 SG 117.6 104.2 REMARK 620 4 HIS A 127 ND1 112.9 104.8 102.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 135 SG REMARK 620 2 CYS A 138 SG 113.4 REMARK 620 3 CYS A 153 SG 109.3 102.6 REMARK 620 4 CYS A 156 SG 106.5 114.2 110.8 REMARK 620 N 1 2 3 DBREF 7OXD A 14 168 PDB 7OXD 7OXD 14 168 SEQRES 1 A 155 PHE LEU ILE LYS PRO TYR GLU GLY GLU SER LEU SER HIS SEQRES 2 A 155 PHE LEU GLY ARG PHE ARG ARG ALA ASN HIS LEU SER ALA SEQRES 3 A 155 SER GLY LEU GLY THR LEU ALA GLY ILE GLY ALA ILE VAL SEQRES 4 A 155 ALA ARG TRP GLU ARG PHE HIS PHE ASN PRO ARG PRO SER SEQRES 5 A 155 GLN GLN GLU LEU GLU ALA ILE ALA SER VAL VAL GLU VAL SEQRES 6 A 155 ASP ALA GLN ARG LEU ALA GLN MET LEU PRO PRO ALA GLY SEQRES 7 A 155 VAL GLY MET GLN HIS GLU PRO ILE ARG LEU CYS GLY ALA SEQRES 8 A 155 CYS TYR ALA GLU SER PRO CYS HIS ARG ILE GLU TRP GLN SEQRES 9 A 155 TYR LYS SER VAL TRP LYS CYS ASP ARG HIS GLN LEU LYS SEQRES 10 A 155 ILE LEU ALA LYS CYS PRO ASN CYS GLN ALA PRO PHE LYS SEQRES 11 A 155 MET PRO ALA LEU TRP GLU ASP GLY CYS CYS HIS ARG CYS SEQRES 12 A 155 ARG MET PRO PHE ALA GLU MET ALA LYS LEU GLN LYS HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *236(H2 O) HELIX 1 AA1 SER A 23 ASN A 35 1 13 HELIX 2 AA2 SER A 38 ALA A 46 1 9 HELIX 3 AA3 ALA A 50 ARG A 57 1 8 HELIX 4 AA4 SER A 65 GLU A 77 1 13 HELIX 5 AA5 ASP A 79 GLN A 85 1 7 HELIX 6 AA6 CYS A 102 SER A 109 1 8 HELIX 7 AA7 ARG A 113 TYR A 118 5 6 HELIX 8 AA8 MET A 144 TRP A 148 5 5 HELIX 9 AA9 PRO A 159 ALA A 164 1 6 HELIX 10 AB1 LYS A 165 GLN A 167 5 3 SHEET 1 AA1 2 LYS A 123 CYS A 124 0 SHEET 2 AA1 2 LEU A 129 LYS A 130 -1 O LEU A 129 N CYS A 124 LINK SG CYS A 102 ZN ZN A 202 1555 1555 2.32 LINK SG CYS A 105 ZN ZN A 202 1555 1555 2.30 LINK SG CYS A 124 ZN ZN A 202 1555 1555 2.31 LINK ND1 HIS A 127 ZN ZN A 202 1555 1555 2.10 LINK SG CYS A 135 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 138 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 153 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 156 ZN ZN A 201 1555 1555 2.29 CISPEP 1 GLU A 97 PRO A 98 0 -14.57 CRYST1 41.636 49.875 86.800 90.00 90.00 90.00 P 21 21 21 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 0.024018 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011521 0.00000