HEADER IMMUNE SYSTEM 02-MAY-10 3MU9 OBSLTE 15-JUN-11 3MU9 3RT4 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDOGLYCAN RECOGNITION PROTEIN TITLE 2 WITH LIPOPOLYSACCHARIDE AT 1.7A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDOGLYCAN RECOGNITION PROTEIN 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PEPTIDOGLYCAN RECOGNITION PROTEIN SHORT, PGRP-S SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELUS DROMEDARIUS; SOURCE 3 ORGANISM_COMMON: DROMEDARY; SOURCE 4 ORGANISM_TAXID: 9838 KEYWDS PGRP, COMPLEX, IMMUNE SYSTEM, LPS EXPDTA X-RAY DIFFRACTION AUTHOR P.SHARMA,N.SINGH,M.SINHA,P.KAUR,S.SHARMA,T.P.SINGH REVDAT 2 15-JUN-11 3MU9 1 OBSLTE REVDAT 1 23-JUN-10 3MU9 0 JRNL AUTH P.SHARMA,N.SINGH,M.SINHA,P.KAUR,S.SHARMA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDOGLYCAN JRNL TITL 2 RECOGNITION PROTEIN WITH LIPOPOLYSACCHARIDE AT 1.7A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 108729.870 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 49.9 REMARK 3 NUMBER OF REFLECTIONS : 78352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2377 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 12514 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 395 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5347 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 613 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.96000 REMARK 3 B22 (A**2) : -5.61000 REMARK 3 B33 (A**2) : -4.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.01 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.520 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.960 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.070 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 40.35 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 5 : LPS.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 5 : LPS.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3MU9 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAY-10. REMARK 100 THE RCSB ID CODE IS RCSB059001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78352 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 32.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 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: AMORE REMARK 200 STARTING MODEL: 3C2X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL, 20% PEG3350, 0.2M NA-K REMARK 280 TARTARATE, PH 8.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.57000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.39500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 80.93000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.57000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.39500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 80.93000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.57000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.39500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 80.93000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.57000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.39500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 80.93000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 CYS D 6 ND2 ASN D 126 2455 1.35 REMARK 500 N GLU C 1 OE1 GLU C 1 3555 1.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 2 N ASP A 2 CA 0.128 REMARK 500 PRO A 3 N PRO A 3 CA 0.149 REMARK 500 ASP A 2 C PRO A 3 N 0.122 REMARK 500 ALA C 171 C ALA C 171 OXT 0.167 REMARK 500 CYS D 49 CB CYS D 49 SG -0.252 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 3 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 PRO A 3 N - CA - C ANGL. DEV. = 21.2 DEGREES REMARK 500 PRO A 3 C - N - CA ANGL. DEV. = 11.4 DEGREES REMARK 500 PRO A 3 C - N - CD ANGL. DEV. = -17.2 DEGREES REMARK 500 TRP B 15 CA - CB - CG ANGL. DEV. = 11.4 DEGREES REMARK 500 ARG B 28 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP C 2 CB - CA - C ANGL. DEV. = 13.9 DEGREES REMARK 500 PRO C 3 C - N - CD ANGL. DEV. = -16.6 DEGREES REMARK 500 PRO C 4 C - N - CD ANGL. DEV. = -13.7 DEGREES REMARK 500 ALA C 5 N - CA - C ANGL. DEV. = -20.1 DEGREES REMARK 500 SER C 8 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 CYS C 130 O - C - N ANGL. DEV. = -11.1 DEGREES REMARK 500 PRO D 3 C - N - CD ANGL. DEV. = -15.7 DEGREES 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 PRO A 4 166.21 -44.92 REMARK 500 CYS A 6 127.87 -174.57 REMARK 500 HIS A 93 -17.81 -151.83 REMARK 500 ASN A 140 41.62 -106.25 REMARK 500 HIS B 93 -15.57 -151.65 REMARK 500 ASN B 140 46.70 -96.21 REMARK 500 PRO C 4 -154.46 -63.11 REMARK 500 CYS C 6 -144.69 -147.19 REMARK 500 ALA C 94 14.95 -141.90 REMARK 500 ASN C 140 43.38 -106.13 REMARK 500 CYS D 6 -81.90 -22.70 REMARK 500 ALA D 39 -1.92 73.53 REMARK 500 HIS D 93 -13.71 -144.83 REMARK 500 TYR D 111 43.95 -103.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 111 0.06 SIDE CHAIN REMARK 500 TYR D 111 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP A 2 24.7 L L OUTSIDE RANGE REMARK 500 PRO A 3 24.1 L L OUTSIDE RANGE 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 407 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH A 538 DISTANCE = 7.07 ANGSTROMS REMARK 525 HOH B 299 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH B 457 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH B 467 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH B 469 DISTANCE = 5.66 ANGSTROMS REMARK 525 HOH B 549 DISTANCE = 5.70 ANGSTROMS REMARK 525 HOH C 223 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH C 307 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH C 499 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH C 503 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH C 578 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH C 639 DISTANCE = 5.22 ANGSTROMS REMARK 525 HOH C 656 DISTANCE = 5.38 ANGSTROMS REMARK 525 HOH C 664 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH C 669 DISTANCE = 5.35 ANGSTROMS REMARK 525 HOH D 224 DISTANCE = 5.36 ANGSTROMS REMARK 525 HOH D 589 DISTANCE = 5.98 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LP5 C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLA C 6748 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C2X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PEPTIDOGLYCAN RECOGNITION PROTEIN AT REMARK 900 1.8A RESOLUTION DBREF 3MU9 A 1 171 UNP Q9GK12 PGRP1_CAMDR 23 193 DBREF 3MU9 B 1 171 UNP Q9GK12 PGRP1_CAMDR 23 193 DBREF 3MU9 C 1 171 UNP Q9GK12 PGRP1_CAMDR 23 193 DBREF 3MU9 D 1 171 UNP Q9GK12 PGRP1_CAMDR 23 193 SEQRES 1 A 171 GLU ASP PRO PRO ALA CYS GLY SER ILE VAL PRO ARG ARG SEQRES 2 A 171 GLU TRP ARG ALA LEU ALA SER GLU CYS ARG GLU ARG LEU SEQRES 3 A 171 THR ARG PRO VAL ARG TYR VAL VAL VAL SER HIS THR ALA SEQRES 4 A 171 GLY SER HIS CYS ASP THR PRO ALA SER CYS ALA GLN GLN SEQRES 5 A 171 ALA GLN ASN VAL GLN SER TYR HIS VAL ARG ASN LEU GLY SEQRES 6 A 171 TRP CYS ASP VAL GLY TYR ASN PHE LEU ILE GLY GLU ASP SEQRES 7 A 171 GLY LEU VAL TYR GLU GLY ARG GLY TRP ASN ILE LYS GLY SEQRES 8 A 171 ALA HIS ALA GLY PRO THR TRP ASN PRO ILE SER ILE GLY SEQRES 9 A 171 ILE SER PHE MET GLY ASN TYR MET ASN ARG VAL PRO PRO SEQRES 10 A 171 PRO ARG ALA LEU ARG ALA ALA GLN ASN LEU LEU ALA CYS SEQRES 11 A 171 GLY VAL ALA LEU GLY ALA LEU ARG SER ASN TYR GLU VAL SEQRES 12 A 171 LYS GLY HIS ARG ASP VAL GLN PRO THR LEU SER PRO GLY SEQRES 13 A 171 ASP ARG LEU TYR GLU ILE ILE GLN THR TRP SER HIS TYR SEQRES 14 A 171 ARG ALA SEQRES 1 B 171 GLU ASP PRO PRO ALA CYS GLY SER ILE VAL PRO ARG ARG SEQRES 2 B 171 GLU TRP ARG ALA LEU ALA SER GLU CYS ARG GLU ARG LEU SEQRES 3 B 171 THR ARG PRO VAL ARG TYR VAL VAL VAL SER HIS THR ALA SEQRES 4 B 171 GLY SER HIS CYS ASP THR PRO ALA SER CYS ALA GLN GLN SEQRES 5 B 171 ALA GLN ASN VAL GLN SER TYR HIS VAL ARG ASN LEU GLY SEQRES 6 B 171 TRP CYS ASP VAL GLY TYR ASN PHE LEU ILE GLY GLU ASP SEQRES 7 B 171 GLY LEU VAL TYR GLU GLY ARG GLY TRP ASN ILE LYS GLY SEQRES 8 B 171 ALA HIS ALA GLY PRO THR TRP ASN PRO ILE SER ILE GLY SEQRES 9 B 171 ILE SER PHE MET GLY ASN TYR MET ASN ARG VAL PRO PRO SEQRES 10 B 171 PRO ARG ALA LEU ARG ALA ALA GLN ASN LEU LEU ALA CYS SEQRES 11 B 171 GLY VAL ALA LEU GLY ALA LEU ARG SER ASN TYR GLU VAL SEQRES 12 B 171 LYS GLY HIS ARG ASP VAL GLN PRO THR LEU SER PRO GLY SEQRES 13 B 171 ASP ARG LEU TYR GLU ILE ILE GLN THR TRP SER HIS TYR SEQRES 14 B 171 ARG ALA SEQRES 1 C 171 GLU ASP PRO PRO ALA CYS GLY SER ILE VAL PRO ARG ARG SEQRES 2 C 171 GLU TRP ARG ALA LEU ALA SER GLU CYS ARG GLU ARG LEU SEQRES 3 C 171 THR ARG PRO VAL ARG TYR VAL VAL VAL SER HIS THR ALA SEQRES 4 C 171 GLY SER HIS CYS ASP THR PRO ALA SER CYS ALA GLN GLN SEQRES 5 C 171 ALA GLN ASN VAL GLN SER TYR HIS VAL ARG ASN LEU GLY SEQRES 6 C 171 TRP CYS ASP VAL GLY TYR ASN PHE LEU ILE GLY GLU ASP SEQRES 7 C 171 GLY LEU VAL TYR GLU GLY ARG GLY TRP ASN ILE LYS GLY SEQRES 8 C 171 ALA HIS ALA GLY PRO THR TRP ASN PRO ILE SER ILE GLY SEQRES 9 C 171 ILE SER PHE MET GLY ASN TYR MET ASN ARG VAL PRO PRO SEQRES 10 C 171 PRO ARG ALA LEU ARG ALA ALA GLN ASN LEU LEU ALA CYS SEQRES 11 C 171 GLY VAL ALA LEU GLY ALA LEU ARG SER ASN TYR GLU VAL SEQRES 12 C 171 LYS GLY HIS ARG ASP VAL GLN PRO THR LEU SER PRO GLY SEQRES 13 C 171 ASP ARG LEU TYR GLU ILE ILE GLN THR TRP SER HIS TYR SEQRES 14 C 171 ARG ALA SEQRES 1 D 171 GLU ASP PRO PRO ALA CYS GLY SER ILE VAL PRO ARG ARG SEQRES 2 D 171 GLU TRP ARG ALA LEU ALA SER GLU CYS ARG GLU ARG LEU SEQRES 3 D 171 THR ARG PRO VAL ARG TYR VAL VAL VAL SER HIS THR ALA SEQRES 4 D 171 GLY SER HIS CYS ASP THR PRO ALA SER CYS ALA GLN GLN SEQRES 5 D 171 ALA GLN ASN VAL GLN SER TYR HIS VAL ARG ASN LEU GLY SEQRES 6 D 171 TRP CYS ASP VAL GLY TYR ASN PHE LEU ILE GLY GLU ASP SEQRES 7 D 171 GLY LEU VAL TYR GLU GLY ARG GLY TRP ASN ILE LYS GLY SEQRES 8 D 171 ALA HIS ALA GLY PRO THR TRP ASN PRO ILE SER ILE GLY SEQRES 9 D 171 ILE SER PHE MET GLY ASN TYR MET ASN ARG VAL PRO PRO SEQRES 10 D 171 PRO ARG ALA LEU ARG ALA ALA GLN ASN LEU LEU ALA CYS SEQRES 11 D 171 GLY VAL ALA LEU GLY ALA LEU ARG SER ASN TYR GLU VAL SEQRES 12 D 171 LYS GLY HIS ARG ASP VAL GLN PRO THR LEU SER PRO GLY SEQRES 13 D 171 ASP ARG LEU TYR GLU ILE ILE GLN THR TRP SER HIS TYR SEQRES 14 D 171 ARG ALA HET LP5 C 501 48 HET TLA C6748 10 HETNAM LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5- HETNAM 2 LP5 ((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY) HETNAM 3 LP5 TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE HETNAM TLA L(+)-TARTARIC ACID FORMUL 5 LP5 C34 H66 N O12 P FORMUL 6 TLA C4 H6 O6 FORMUL 7 HOH *613(H2 O) HELIX 1 1 PRO A 11 ARG A 16 5 6 HELIX 2 2 THR A 45 ASN A 63 1 19 HELIX 3 3 ALA A 94 ASN A 99 1 6 HELIX 4 4 PRO A 117 LEU A 134 1 18 HELIX 5 5 ARG A 147 VAL A 149 5 3 HELIX 6 6 GLY A 156 GLN A 164 1 9 HELIX 7 7 THR B 45 ASN B 63 1 19 HELIX 8 8 ALA B 94 ASN B 99 1 6 HELIX 9 9 PRO B 117 LEU B 134 1 18 HELIX 10 10 HIS B 146 GLN B 150 1 5 HELIX 11 11 GLY B 156 GLN B 164 1 9 HELIX 12 12 THR C 45 ASN C 63 1 19 HELIX 13 13 ALA C 94 ASN C 99 1 6 HELIX 14 14 PRO C 117 LEU C 134 1 18 HELIX 15 15 ARG C 147 VAL C 149 5 3 HELIX 16 16 GLY C 156 GLN C 164 1 9 HELIX 17 17 THR D 45 ASN D 63 1 19 HELIX 18 18 ALA D 94 ASN D 99 1 6 HELIX 19 19 PRO D 117 LEU D 134 1 18 HELIX 20 20 HIS D 146 GLN D 150 1 5 HELIX 21 21 GLY D 156 GLN D 164 1 9 SHEET 1 A 6 ILE A 9 VAL A 10 0 SHEET 2 A 6 VAL A 81 GLU A 83 1 O VAL A 81 N VAL A 10 SHEET 3 A 6 PHE A 73 ILE A 75 -1 N LEU A 74 O TYR A 82 SHEET 4 A 6 SER A 102 PHE A 107 1 O SER A 106 N ILE A 75 SHEET 5 A 6 VAL A 30 HIS A 37 1 N SER A 36 O ILE A 105 SHEET 6 A 6 LEU A 137 GLY A 145 1 O LYS A 144 N VAL A 33 SHEET 1 B 5 VAL B 81 GLU B 83 0 SHEET 2 B 5 PHE B 73 ILE B 75 -1 N LEU B 74 O TYR B 82 SHEET 3 B 5 SER B 102 PHE B 107 1 O SER B 106 N ILE B 75 SHEET 4 B 5 VAL B 30 HIS B 37 1 N SER B 36 O PHE B 107 SHEET 5 B 5 LEU B 137 GLY B 145 1 O LYS B 144 N VAL B 33 SHEET 1 C 6 ILE C 9 VAL C 10 0 SHEET 2 C 6 VAL C 81 GLU C 83 1 O VAL C 81 N VAL C 10 SHEET 3 C 6 PHE C 73 ILE C 75 -1 N LEU C 74 O TYR C 82 SHEET 4 C 6 SER C 102 PHE C 107 1 O SER C 106 N ILE C 75 SHEET 5 C 6 VAL C 30 HIS C 37 1 N VAL C 34 O ILE C 103 SHEET 6 C 6 LEU C 137 GLY C 145 1 O LYS C 144 N VAL C 33 SHEET 1 D 6 ILE D 9 VAL D 10 0 SHEET 2 D 6 VAL D 81 GLU D 83 1 O VAL D 81 N VAL D 10 SHEET 3 D 6 PHE D 73 ILE D 75 -1 N LEU D 74 O TYR D 82 SHEET 4 D 6 SER D 102 PHE D 107 1 O SER D 106 N ILE D 75 SHEET 5 D 6 VAL D 30 HIS D 37 1 N VAL D 34 O ILE D 103 SHEET 6 D 6 LEU D 137 GLY D 145 1 O GLU D 142 N ARG D 31 SSBOND 1 CYS A 6 CYS A 130 1555 1555 2.03 SSBOND 2 CYS A 22 CYS A 67 1555 1555 2.06 SSBOND 3 CYS A 43 CYS A 49 1555 1555 1.98 SSBOND 4 CYS B 6 CYS B 130 1555 1555 1.93 SSBOND 5 CYS B 22 CYS B 67 1555 1555 2.03 SSBOND 6 CYS B 43 CYS B 49 1555 1555 2.15 SSBOND 7 CYS C 6 CYS C 130 1555 1555 1.73 SSBOND 8 CYS C 22 CYS C 67 1555 1555 2.06 SSBOND 9 CYS C 43 CYS C 49 1555 1555 2.09 SSBOND 10 CYS D 6 CYS D 130 1555 1555 1.89 SSBOND 11 CYS D 22 CYS D 67 1555 1555 2.03 SSBOND 12 CYS D 43 CYS D 49 1555 1555 2.25 CISPEP 1 ARG A 28 PRO A 29 0 3.07 CISPEP 2 SER A 154 PRO A 155 0 0.19 CISPEP 3 ARG B 28 PRO B 29 0 -0.92 CISPEP 4 SER B 154 PRO B 155 0 2.22 CISPEP 5 ARG C 28 PRO C 29 0 1.85 CISPEP 6 SER C 154 PRO C 155 0 0.70 CISPEP 7 ARG D 28 PRO D 29 0 -0.01 CISPEP 8 SER D 154 PRO D 155 0 14.40 SITE 1 AC1 33 ARG A 170 LEU C 64 TRP C 66 LYS C 90 SITE 2 AC1 33 ALA C 92 HIS C 93 ALA C 94 GLY C 95 SITE 3 AC1 33 PRO C 96 ASN C 99 PRO C 100 GLN C 150 SITE 4 AC1 33 PRO C 151 HOH C 178 HOH C 210 HOH C 421 SITE 5 AC1 33 HOH C 584 ALA D 92 HIS D 93 ALA D 94 SITE 6 AC1 33 GLY D 95 THR D 97 TRP D 98 ASN D 99 SITE 7 AC1 33 LYS D 144 ASP D 148 VAL D 149 GLN D 150 SITE 8 AC1 33 PRO D 151 ALA D 171 HOH D 180 HOH D 423 SITE 9 AC1 33 HOH D 534 SITE 1 AC2 11 HIS C 37 ALA C 39 THR C 152 LEU C 153 SITE 2 AC2 11 SER C 154 HOH C 399 HIS D 37 ALA D 39 SITE 3 AC2 11 THR D 152 LEU D 153 SER D 154 CRYST1 87.140 100.790 161.860 90.00 90.00 90.00 I 2 2 2 32 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 0.011476 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009922 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006178 0.00000