HEADER IMMUNE SYSTEM 11-MAY-15 4ZQV TITLE CDII IMMUNITY PROTEIN FROM YERSINIA KRISTENSENII COMPND MOL_ID: 1; COMPND 2 MOLECULE: CDII IMMUNITY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA KRISTENSENII ATCC 33638; SOURCE 3 ORGANISM_TAXID: 527012; SOURCE 4 GENE: YKRIS0001_10740; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS IMMUNITY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.P.MORSE,C.W.GOULDING REVDAT 5 27-SEP-23 4ZQV 1 REMARK REVDAT 4 25-DEC-19 4ZQV 1 REMARK REVDAT 3 13-SEP-17 4ZQV 1 JRNL REMARK REVDAT 2 02-DEC-15 4ZQV 1 JRNL REVDAT 1 28-OCT-15 4ZQV 0 JRNL AUTH R.P.MORSE,J.L.WILLETT,P.M.JOHNSON,J.ZHENG,A.CREDALI, JRNL AUTH 2 A.INIGUEZ,J.S.NOWICK,C.S.HAYES,C.W.GOULDING JRNL TITL DIVERSIFICATION OF BETA-AUGMENTATION INTERACTIONS BETWEEN JRNL TITL 2 CDI TOXIN/IMMUNITY PROTEINS. JRNL REF J.MOL.BIOL. V. 427 3766 2015 JRNL REFN ESSN 1089-8638 JRNL PMID 26449640 JRNL DOI 10.1016/J.JMB.2015.09.020 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 16580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1673 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 1.8561 - 1.8031 1.00 1223 142 0.2239 0.2804 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.110 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 : 0.007 1309 REMARK 3 ANGLE : 0.998 1776 REMARK 3 CHIRALITY : 0.040 200 REMARK 3 PLANARITY : 0.005 230 REMARK 3 DIHEDRAL : 10.713 478 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 4ZQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000201393. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16618 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4800 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: NULL REMARK 200 STARTING MODEL: 4G6U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 20% PEG 3350, REMARK 280 PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.15733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.31467 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 THR A 166 REMARK 465 SER A 167 REMARK 465 LEU A 168 REMARK 465 GLU A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 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 LYS A 4 CG CD CE NZ REMARK 470 GLU A 67 CG CD OE1 OE2 REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 LYS A 126 CG CD CE NZ REMARK 470 LYS A 136 CG CD CE NZ 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 LEU A 27 90.92 -160.10 REMARK 500 GLU A 125 -93.01 -88.36 REMARK 500 REMARK 500 REMARK: NULL DBREF 4ZQV A 1 165 UNP C4TS51 C4TS51_YERKR 1 165 SEQADV 4ZQV THR A 84 UNP C4TS51 ALA 84 CONFLICT SEQADV 4ZQV THR A 166 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV SER A 167 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV LEU A 168 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV GLU A 169 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV HIS A 170 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV HIS A 171 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV HIS A 172 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV HIS A 173 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV HIS A 174 UNP C4TS51 EXPRESSION TAG SEQADV 4ZQV HIS A 175 UNP C4TS51 EXPRESSION TAG SEQRES 1 A 175 MET PHE ASN LYS ASP GLN ASP TYR TRP VAL SER VAL TYR SEQRES 2 A 175 SER THR LYS ASP PHE LEU SER VAL GLU THR ASP SER GLY SEQRES 3 A 175 LEU GLY ARG VAL ARG ARG ASP PRO LEU PHE PRO SER HIS SEQRES 4 A 175 LEU LEU PRO PRO ASP ALA ASP ASN GLN THR ILE GLY ASP SEQRES 5 A 175 ALA VAL LEU ILE ALA LEU SER ASN SER ARG THR LEU SER SEQRES 6 A 175 LEU GLU GLU SER ALA ASP PHE PHE ASP LEU GLU THR GLY SEQRES 7 A 175 LYS GLU GLN TYR ALA THR TRP ILE ALA MET LEU MET GLU SEQRES 8 A 175 LYS TYR GLY TYR LYS THR LYS ARG ALA LEU PHE LYS ASP SEQRES 9 A 175 MET LYS ASN CYS SER ILE HIS CYS ILE ASN ASP LEU ILE SEQRES 10 A 175 THR ILE SER PRO THR ARG HIS GLU LYS LEU GLU ALA TRP SEQRES 11 A 175 SER GLY ARG GLY ILE LYS GLU SER ASP ASP VAL VAL ILE SEQRES 12 A 175 PRO ALA ASP SER ILE PRO GLU GLU ILE GLY ALA ALA LEU SEQRES 13 A 175 ARG LEU ALA LEU SER ARG CYS LYS GLY THR SER LEU GLU SEQRES 14 A 175 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *130(H2 O) HELIX 1 AA1 ASP A 46 SER A 61 1 16 HELIX 2 AA2 SER A 65 PHE A 73 1 9 HELIX 3 AA3 ASP A 74 GLY A 94 1 21 HELIX 4 AA4 THR A 97 LYS A 103 1 7 HELIX 5 AA5 LYS A 136 ASP A 140 5 5 HELIX 6 AA6 ILE A 148 ARG A 162 1 15 SHEET 1 AA1 3 VAL A 30 ARG A 32 0 SHEET 2 AA1 3 LEU A 19 GLY A 26 -1 N SER A 25 O ARG A 31 SHEET 3 AA1 3 HIS A 39 LEU A 41 -1 O LEU A 41 N LEU A 19 SHEET 1 AA2 6 VAL A 30 ARG A 32 0 SHEET 2 AA2 6 LEU A 19 GLY A 26 -1 N SER A 25 O ARG A 31 SHEET 3 AA2 6 TYR A 8 SER A 14 -1 N TYR A 13 O SER A 20 SHEET 4 AA2 6 LYS A 106 ILE A 113 -1 O ILE A 110 N VAL A 10 SHEET 5 AA2 6 LEU A 116 SER A 120 -1 O THR A 118 N HIS A 111 SHEET 6 AA2 6 VAL A 141 PRO A 144 -1 O ILE A 143 N ILE A 117 SHEET 1 AA3 2 ARG A 123 HIS A 124 0 SHEET 2 AA3 2 TRP A 130 SER A 131 -1 O SER A 131 N ARG A 123 CRYST1 54.448 54.448 54.472 90.00 90.00 120.00 P 31 3 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 0.018366 0.010604 0.000000 0.00000 SCALE2 0.000000 0.021207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018358 0.00000