HEADER CHAPERONE 18-JUN-22 7Y6B TITLE CRYSTAL STRUCTURE OF THE ESCE/ESAH COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESCE/YSCE/SSAE FAMILY TYPE III SECRETION SYSTEM NEEDLE COMPND 3 PROTEIN CO-CHAPERONE; COMPND 4 CHAIN: A, D; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: NCBI REFERENCE SEQUENCE WP_012847727.1; PLGS IS COMPND 7 EXPRESSION TAG; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ESCG/YSCG/SSAH FAMILY TYPE III SECRETION SYSTEM NEEDLE COMPND 10 PROTEIN CO-CHAPERONE; COMPND 11 CHAIN: B, E; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: GENBANK ADM40922.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EDWARDSIELLA PISCICIDA; SOURCE 3 ORGANISM_TAXID: 1263550; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: EDWARDSIELLA PISCICIDA; SOURCE 8 ORGANISM_TAXID: 1263550; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ESCE, ESAH, TYPE III SECRETION SYSTEM, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR Z.X.ZENG,S.B.XIAO,L.J.LIAO,Y.Z.ZHOU REVDAT 3 29-MAY-24 7Y6B 1 REMARK REVDAT 2 28-SEP-22 7Y6B 1 JRNL REVDAT 1 20-JUL-22 7Y6B 0 JRNL AUTH Z.X.ZENG,L.Y.LIU,S.B.XIAO,J.F.LU,Y.L.LIU,J.LI,Y.Z.ZHOU, JRNL AUTH 2 L.J.LIAO,D.Y.LI,Y.ZHOU,P.NIE,H.X.XIE JRNL TITL SECRETED IN A TYPE III SECRETION SYSTEM-DEPENDENT MANNER, JRNL TITL 2 ESAH AND ESCE ARE THE COCHAPERONES OF THE T3SS NEEDLE JRNL TITL 3 PROTEIN ESAG OF EDWARDSIELLA PISCICIDA. JRNL REF MBIO V. 13 25022 2022 JRNL REFN ESSN 2150-7511 JRNL PMID 35861543 JRNL DOI 10.1128/MBIO.01250-22 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 31937 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1567 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 39.5680 - 4.0020 0.97 2779 146 0.1879 0.2128 REMARK 3 2 4.0020 - 3.1769 0.98 2767 151 0.1864 0.2135 REMARK 3 3 3.1769 - 2.7755 0.99 2777 116 0.2059 0.2192 REMARK 3 4 2.7755 - 2.5217 0.99 2748 159 0.2024 0.2155 REMARK 3 5 2.5217 - 2.3410 0.99 2745 149 0.1947 0.2417 REMARK 3 6 2.3410 - 2.2030 0.99 2761 145 0.1960 0.2470 REMARK 3 7 2.2030 - 2.0927 0.99 2793 126 0.1870 0.2012 REMARK 3 8 2.0927 - 2.0016 0.99 2757 121 0.2058 0.2477 REMARK 3 9 2.0016 - 1.9245 0.99 2712 162 0.2195 0.2578 REMARK 3 10 1.9245 - 1.8581 0.99 2781 135 0.2333 0.2906 REMARK 3 11 1.8581 - 1.8000 1.00 2750 157 0.2700 0.2753 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.85 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 7Y6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100.000 REMARK 200 PH : 6.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31956 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 (%): 49.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M KSCN, 0.1 M TRIS PH 8.4, 23% REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, 3%(W/V) 1,6- REMARK 280 HEXANEDIOL, PH 6.20, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.37500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 PRO A 1 REMARK 465 PRO B 69 REMARK 465 ASP B 70 REMARK 465 ASP B 71 REMARK 465 CYS B 72 REMARK 465 LEU B 73 REMARK 465 PRO B 74 REMARK 465 LEU B 75 REMARK 465 ARG B 76 REMARK 465 ALA B 77 REMARK 465 LEU B 78 REMARK 465 LEU B 79 REMARK 465 THR B 80 REMARK 465 PRO B 81 REMARK 465 THR B 82 REMARK 465 THR B 83 REMARK 465 GLN B 84 REMARK 465 GLU B 85 REMARK 465 LYS B 86 REMARK 465 THR B 87 REMARK 465 ARG B 88 REMARK 465 GLY D 73 REMARK 465 ASP E 2 REMARK 465 THR E 3 REMARK 465 LEU E 78 REMARK 465 LEU E 79 REMARK 465 THR E 80 REMARK 465 PRO E 81 REMARK 465 THR E 82 REMARK 465 THR E 83 REMARK 465 GLN E 84 REMARK 465 GLU E 85 REMARK 465 LYS E 86 REMARK 465 THR E 87 REMARK 465 ARG E 88 DBREF 7Y6B A 1 73 PDB 7Y6B 7Y6B 1 73 DBREF 7Y6B B 2 88 PDB 7Y6B 7Y6B 2 88 DBREF 7Y6B D 1 73 PDB 7Y6B 7Y6B 1 73 DBREF 7Y6B E 2 88 PDB 7Y6B 7Y6B 2 88 SEQRES 1 A 73 PRO LEU GLY SER THR HIS LEU GLU ASP SER LEU ARG HIS SEQRES 2 A 73 ASP PRO ARG GLY HIS GLN ARG GLN ARG LEU ILE ASP CYS SEQRES 3 A 73 LEU ASN GLU ALA ALA ARG ARG LEU ALA LEU GLU LEU ARG SEQRES 4 A 73 GLN PRO HIS SER ALA ASP GLU TYR ALA ARG LEU GLU ARG SEQRES 5 A 73 GLN ARG GLN SER CYS LEU ALA ALA VAL ARG VAL ILE ASP SEQRES 6 A 73 THR LEU TRP THR LEU HIS GLN GLY SEQRES 1 B 87 ASP THR LEU SER VAL PRO HIS LEU VAL VAL GLU ALA GLY SEQRES 2 B 87 PHE ALA ALA VAL ASN CYS GLY MET ARG ALA GLU MET HIS SEQRES 3 B 87 ASP ILE LEU ASN ALA LEU PRO ASP TRP LEU ASP ASP PRO SEQRES 4 B 87 ASP GLN VAL THR ARG CYS GLU ALA ILE LEU LEU PHE GLY SEQRES 5 B 87 LEU GLY ARG GLN ARG ALA ALA ALA ALA ARG LEU ALA MET SEQRES 6 B 87 LEU PRO PRO ASP ASP CYS LEU PRO LEU ARG ALA LEU LEU SEQRES 7 B 87 THR PRO THR THR GLN GLU LYS THR ARG SEQRES 1 D 73 PRO LEU GLY SER THR HIS LEU GLU ASP SER LEU ARG HIS SEQRES 2 D 73 ASP PRO ARG GLY HIS GLN ARG GLN ARG LEU ILE ASP CYS SEQRES 3 D 73 LEU ASN GLU ALA ALA ARG ARG LEU ALA LEU GLU LEU ARG SEQRES 4 D 73 GLN PRO HIS SER ALA ASP GLU TYR ALA ARG LEU GLU ARG SEQRES 5 D 73 GLN ARG GLN SER CYS LEU ALA ALA VAL ARG VAL ILE ASP SEQRES 6 D 73 THR LEU TRP THR LEU HIS GLN GLY SEQRES 1 E 87 ASP THR LEU SER VAL PRO HIS LEU VAL VAL GLU ALA GLY SEQRES 2 E 87 PHE ALA ALA VAL ASN CYS GLY MET ARG ALA GLU MET HIS SEQRES 3 E 87 ASP ILE LEU ASN ALA LEU PRO ASP TRP LEU ASP ASP PRO SEQRES 4 E 87 ASP GLN VAL THR ARG CYS GLU ALA ILE LEU LEU PHE GLY SEQRES 5 E 87 LEU GLY ARG GLN ARG ALA ALA ALA ALA ARG LEU ALA MET SEQRES 6 E 87 LEU PRO PRO ASP ASP CYS LEU PRO LEU ARG ALA LEU LEU SEQRES 7 E 87 THR PRO THR THR GLN GLU LYS THR ARG FORMUL 5 HOH *114(H2 O) HELIX 1 AA1 THR A 5 HIS A 13 1 9 HELIX 2 AA2 GLY A 17 ARG A 39 1 23 HELIX 3 AA3 SER A 43 GLY A 73 1 31 HELIX 4 AA4 ASP B 2 LEU B 4 5 3 HELIX 5 AA5 SER B 5 ASN B 19 1 15 HELIX 6 AA6 MET B 22 LEU B 37 1 16 HELIX 7 AA7 ASP B 39 GLY B 55 1 17 HELIX 8 AA8 ARG B 56 ALA B 65 1 10 HELIX 9 AA9 THR D 5 HIS D 13 1 9 HELIX 10 AB1 GLY D 17 ARG D 39 1 23 HELIX 11 AB2 SER D 43 GLN D 72 1 30 HELIX 12 AB3 SER E 5 GLY E 21 1 17 HELIX 13 AB4 MET E 22 LEU E 37 1 16 HELIX 14 AB5 ASP E 39 GLY E 55 1 17 HELIX 15 AB6 ARG E 56 LEU E 67 1 12 HELIX 16 AB7 PRO E 68 ARG E 76 1 9 CRYST1 55.550 52.750 65.510 90.00 114.03 90.00 P 1 21 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 0.018002 0.000000 0.008026 0.00000 SCALE2 0.000000 0.018957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016713 0.00000