HEADER PROTEIN BINDING 30-JAN-25 9N3A TITLE N-TERMINAL DOMAIN OF CRISPR-ASSOCIATED DING COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED DING; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CASDING; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3) KEYWDS TYPE IV CRISPR, DING, CSF COMPLEX, NTD, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR O.REDMAN,R.N.JACKSON REVDAT 1 09-SEP-26 9N3A 0 JRNL AUTH K.A.KIERNAN,A.A.WILLIAMS,O.REDMAN,E.JENKINS,D.W.TAYLOR, JRNL AUTH 2 R.N.JACKSON JRNL TITL LOCKED AND LOADED: MECHANISMS OF CASDING RECRUITMENT TO THE JRNL TITL 2 TYPE IV-A1 CRISPR EFFECTOR COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2-5419 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 73.3 REMARK 3 NUMBER OF REFLECTIONS : 18481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 904 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 26.8700 - 2.8200 0.98 3888 224 0.1259 0.1417 REMARK 3 2 2.8200 - 2.2400 0.98 3929 205 0.1231 0.1603 REMARK 3 3 2.2400 - 1.9600 0.98 3928 172 0.1324 0.1726 REMARK 3 4 1.9500 - 1.7800 0.91 3674 184 0.1456 0.2126 REMARK 3 5 1.7800 - 1.6500 0.42 1671 83 0.1749 0.1925 REMARK 3 6 1.6500 - 1.5500 0.12 487 36 0.1976 0.1603 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.111 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.081 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.60 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 : 0.008 752 REMARK 3 ANGLE : 0.960 1033 REMARK 3 CHIRALITY : 0.051 125 REMARK 3 PLANARITY : 0.011 131 REMARK 3 DIHEDRAL : 13.625 275 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 9N3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000292385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 2021.11.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.15, POINTLESS REMARK 200 1.12.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18483 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 26.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.3 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 35.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.08 REMARK 200 R MERGE FOR SHELL (I) : 0.03700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 45.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: TABULAR REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOTHER LIQUOR CONSISTED OF 18% PEG REMARK 280 3350, 0.1M NA CITRATE BUFFER (PH 4.0), AND 0.2M AMMONIUM REMARK 280 SULFATE. MOTHER LIQUOR WAS MIXED WITH CONCENTRATED PROTEIN (12 REMARK 280 MG/ML) AT A RATIO OF 2:1.5 (PROTEIN SOLUTION : ML), VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 10.18080 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.65200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.38754 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 10.18080 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.65200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 41.38754 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 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 SER A 1 REMARK 465 SER A 95 REMARK 465 GLY A 96 REMARK 465 SER A 97 REMARK 465 VAL A 98 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 94 CG CD OE1 OE2 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 O HOH A 219 O HOH A 221 2.03 REMARK 500 O HOH A 281 O HOH A 313 2.10 REMARK 500 O HOH A 306 O HOH A 312 2.14 REMARK 500 O HOH A 205 O HOH A 265 2.16 REMARK 500 O ASN A 2 O HOH A 201 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 293 O HOH A 298 4555 1.73 REMARK 500 O HOH A 315 O HOH A 316 4555 2.13 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9N3A A 3 98 UNP A0AA82WPF0_PSEAI DBREF2 9N3A A A0AA82WPF0 23 118 SEQADV 9N3A SER A 1 UNP A0AA82WPF EXPRESSION TAG SEQADV 9N3A ASN A 2 UNP A0AA82WPF EXPRESSION TAG SEQRES 1 A 98 SER ASN MET LYS LEU ALA GLN GLY ALA PHE VAL ASP VAL SEQRES 2 A 98 ILE ARG ILE GLY ALA LEU SER PRO PRO THR ASP GLN ARG SEQRES 3 A 98 SER LEU TRP ALA ARG THR LEU LEU SER GLU ALA VAL ASP SEQRES 4 A 98 GLN GLY LEU ASP SER LEU PRO VAL PRO LEU GLN ASP VAL SEQRES 5 A 98 SER THR PHE THR VAL THR LEU GLN PRO ALA LEU ALA VAL SEQRES 6 A 98 ARG LEU LYS ALA LEU ALA ASP GLN HIS ASN THR PRO VAL SEQRES 7 A 98 SER VAL TYR ALA ALA GLY LEU ILE GLU ALA MET ARG ARG SEQRES 8 A 98 ARG SER GLU SER GLY SER VAL HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 A 103 5 HET SO4 A 104 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *126(H2 O) HELIX 1 AA1 MET A 3 GLY A 8 5 6 HELIX 2 AA2 GLN A 25 GLN A 40 1 16 HELIX 3 AA3 PRO A 48 GLN A 50 5 3 HELIX 4 AA4 GLN A 60 HIS A 74 1 15 HELIX 5 AA5 PRO A 77 GLU A 94 1 18 SHEET 1 AA1 2 ASP A 12 LEU A 19 0 SHEET 2 AA1 2 VAL A 52 LEU A 59 -1 O PHE A 55 N ILE A 16 CRYST1 27.669 39.304 83.097 90.00 95.05 90.00 I 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 0.036142 0.000000 0.003191 0.00000 SCALE2 0.000000 0.025443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012081 0.00000 CONECT 1476 1477 1478 1479 1480 CONECT 1477 1476 CONECT 1478 1476 CONECT 1479 1476 CONECT 1480 1476 CONECT 1481 1482 1483 1484 1485 CONECT 1482 1481 CONECT 1483 1481 CONECT 1484 1481 CONECT 1485 1481 CONECT 1486 1487 1488 1489 1490 CONECT 1487 1486 CONECT 1488 1486 CONECT 1489 1486 CONECT 1490 1486 CONECT 1491 1492 1493 1494 1495 CONECT 1492 1491 CONECT 1493 1491 CONECT 1494 1491 CONECT 1495 1491 MASTER 251 0 4 5 2 0 0 6 849 1 20 8 END