HEADER IMMUNE SYSTEM 28-FEB-18 6CKH TITLE MANDUCA SEXTA PEPTIDOGLYCAN RECOGNITION PROTEIN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDOGLYCAN-RECOGNITION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MANDUCA SEXTA; SOURCE 3 ORGANISM_COMMON: TOBACCO HAWKMOTH; SOURCE 4 ORGANISM_TAXID: 7130; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PATTERN RECOGNITION RECEPTOR, PEPTIDOGLYCAN, INNATE IMMUNE SYSTEM, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Y.HU REVDAT 2 04-OCT-23 6CKH 1 REMARK REVDAT 1 05-JUN-19 6CKH 0 JRNL AUTH Y.HU,X.CAO,X.LI,Y.WANG,G.J.BOONS,J.DENG,H.JIANG JRNL TITL THE THREE-DIMENSIONAL STRUCTURE AND RECOGNITION MECHANISM OF JRNL TITL 2 MANDUCA SEXTA PEPTIDOGLYCAN RECOGNITION PROTEIN-1. JRNL REF INSECT BIOCHEM.MOL.BIOL. V. 108 44 2019 JRNL REFN ISSN 0965-1748 JRNL PMID 30905759 JRNL DOI 10.1016/J.IBMB.2019.03.001 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 10135 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 2.1700 - 2.1000 0.81 810 0 0.2180 0.2020 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 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 6CKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10140 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : 0.13000 REMARK 200 FOR THE DATA SET : 9.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37900 REMARK 200 FOR SHELL : 2.470 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: 1S2J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 20% (W/V) PEG REMARK 280 3350, PH 6.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 31.86700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.23450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.86700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.23450 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 288 LIES ON A SPECIAL POSITION. 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 HIS A 1 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 23 CD NE REMARK 480 LYS A 26 NZ REMARK 480 ASP A 39 CG OD1 OD2 REMARK 480 LYS A 119 NZ REMARK 480 LYS A 136 CE NZ REMARK 480 LYS A 152 CG CD CE NZ REMARK 480 LYS A 171 CE 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 ASN A 3 31.25 -79.75 REMARK 500 TYR A 90 126.23 75.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 6CKH A 2 172 UNP Q86RS6 Q86RS6_MANSE 21 191 SEQADV 6CKH HIS A 1 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH LEU A 173 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH GLU A 174 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH HIS A 175 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH HIS A 176 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH HIS A 177 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH HIS A 178 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH HIS A 179 UNP Q86RS6 EXPRESSION TAG SEQADV 6CKH HIS A 180 UNP Q86RS6 EXPRESSION TAG SEQRES 1 A 180 HIS CYS ASN VAL VAL SER LYS ASP ASP TRP ASP GLY ILE SEQRES 2 A 180 THR SER VAL HIS ILE GLU TYR LEU THR ARG PRO ILE LYS SEQRES 3 A 180 LEU VAL ILE ILE GLN HIS THR ASP THR PRO GLY CYS ASP SEQRES 4 A 180 THR ASP ASP ALA CYS ALA ALA ARG VAL ARG SER ILE GLN SEQRES 5 A 180 ASP TYR HIS LEU ASP THR LEU ASN TYR TRP ASP ILE GLY SEQRES 6 A 180 SER SER PHE LEU ILE GLY GLY ASN GLY LYS VAL TYR GLU SEQRES 7 A 180 GLY SER GLY TRP LEU HIS VAL GLY VAL PRO ASN TYR ALA SEQRES 8 A 180 TYR ASN ARG LYS ALA ILE LYS ILE THR PHE ILE GLY SER SEQRES 9 A 180 TYR ASN SER LYS GLU PRO ASN SER GLN GLN LEU ASN ALA SEQRES 10 A 180 ILE LYS ALA LEU LEU LYS CYS GLY VAL ASP ASN GLY HIS SEQRES 11 A 180 LEU SER SER ASP TYR LYS VAL VAL GLY HIS ARG GLN LEU SEQRES 12 A 180 LEU ASP THR ASP SER PRO GLY ARG LYS LEU TYR ASN ILE SEQRES 13 A 180 ILE ARG ARG TRP PRO GLU TRP THR ASN ASP VAL SER GLU SEQRES 14 A 180 TYR LYS ASP LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *177(H2 O) HELIX 1 AA1 SER A 6 ASP A 11 5 6 HELIX 2 AA2 THR A 40 THR A 58 1 19 HELIX 3 AA3 TYR A 90 LYS A 95 5 6 HELIX 4 AA4 ASN A 111 ASN A 128 1 18 HELIX 5 AA5 ARG A 141 LEU A 143 5 3 HELIX 6 AA6 GLY A 150 ARG A 159 1 10 HELIX 7 AA7 VAL A 167 HIS A 176 1 10 SHEET 1 AA1 5 VAL A 76 GLU A 78 0 SHEET 2 AA1 5 PHE A 68 ILE A 70 -1 N LEU A 69 O TYR A 77 SHEET 3 AA1 5 ILE A 97 PHE A 101 1 O THR A 100 N ILE A 70 SHEET 4 AA1 5 ILE A 25 HIS A 32 1 N ILE A 29 O ILE A 97 SHEET 5 AA1 5 LEU A 131 GLY A 139 1 O LYS A 136 N LYS A 26 SSBOND 1 CYS A 2 CYS A 124 1555 1555 2.03 SSBOND 2 CYS A 38 CYS A 44 1555 1555 2.03 CISPEP 1 ARG A 23 PRO A 24 0 -0.92 CISPEP 2 SER A 148 PRO A 149 0 10.29 CRYST1 63.734 46.469 62.363 90.00 103.05 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 0.015690 0.000000 0.003637 0.00000 SCALE2 0.000000 0.021520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016460 0.00000