10 20 30 40 50 60 70 80 2R90 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER IMMUNE SYSTEM 12-SEP-07 2R90
TITLE CRYSTAL STRUCTURE OF CAMELINE PEPTIDOGLYCAN RECOGNITION TITLE 2 PROTEIN AT 2.8A RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDOGLYCAN RECOGNITION PROTEIN; 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: ARABIAN CAMEL; SOURCE 4 ORGANISM_TAXID: 9838
KEYWDS ANTI BACTERIAL ACTIVITY, IMMUNE SYSTEM, ANTIBIOTIC, KEYWDS 2 ANTIMICROBIAL, IMMUNE RESPONSE, SECRETED
EXPDTA X-RAY DIFFRACTION
AUTHOR P.SHARMA,N.SINGH,M.SINHA,S.SHARMA,P.KAUR,A.SRINIVASAN, AUTHOR 2 T.P.SINGH
REVDAT 2 24-FEB-09 2R90 1 VERSN REVDAT 1 25-SEP-07 2R90 0
JRNL AUTH P.SHARMA,N.SINGH,M.SINHA,S.SHARMA,P.KAUR, JRNL AUTH 2 A.SRINIVASAN,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF CAMELINE PEPTIDOGLYCAN JRNL TITL 2 RECOGNITION PROTEIN AT 2.8A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 79162.650 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 18117 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) : 0.205 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 879 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2796 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 131 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 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 : 0 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.01000 REMARK 3 B22 (A**2) : -11.18000 REMARK 3 B33 (A**2) : -1.84000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.47 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.54 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.64 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) : 1.330 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.620 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.620 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 48.54 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 5 : CARBOHYDRATE.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 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2R90 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-SEP-07. REMARK 100 THE RCSB ID CODE IS RCSB044575.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 6.8 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54132 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18117 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 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 <I/SIGMA(I)> 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: 1YCK REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM TARTARATE, 20% PEG3350, REMARK 280 PH 6.8, 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 44.92450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.18500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 82.05550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.92450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.18500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 82.05550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.92450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.18500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 82.05550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.92450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.18500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.05550 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 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 C 192 LIES ON A SPECIAL POSITION.
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 CG ASP D 2 OD1 ASP D 2 2565 1.21 REMARK 500 CG ASP D 2 CG ASP D 2 2565 1.88 REMARK 500 OH TYR A 59 CB PRO D 4 7545 2.09 REMARK 500 OH TYR A 59 CG PRO D 4 7545 2.11 REMARK 500 CB ASP D 2 OD1 ASP D 2 2565 2.14 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 ARG A 13 CG ARG A 13 CD 0.173 REMARK 500 ARG A 23 CB ARG A 23 CG 0.247 REMARK 500 ARG A 23 CG ARG A 23 CD 0.253 REMARK 500 TYR A 59 CB TYR A 59 CG 0.116 REMARK 500 GLU B 1 CB GLU B 1 CG 0.137 REMARK 500 PRO C 3 CA PRO C 3 C 0.162 REMARK 500 PRO C 4 CD PRO C 4 N 0.125 REMARK 500 PRO C 3 C PRO C 4 N 0.115 REMARK 500 SER C 154 CA SER C 154 CB 0.114 REMARK 500 PRO D 3 N PRO D 3 CA 0.106 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 ASP A 2 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 ASP A 2 N - CA - C ANGL. DEV. = 18.7 DEGREES REMARK 500 PRO A 3 CA - N - CD ANGL. DEV. = -10.4 DEGREES REMARK 500 PRO A 3 C - N - CD ANGL. DEV. = -14.1 DEGREES REMARK 500 PRO A 4 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG A 13 CB - CG - CD ANGL. DEV. = 16.3 DEGREES REMARK 500 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 HIS A 37 CA - CB - CG ANGL. DEV. = 11.6 DEGREES REMARK 500 TYR A 59 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 LEU A 153 CA - C - N ANGL. DEV. = 21.7 DEGREES REMARK 500 LEU A 153 O - C - N ANGL. DEV. = -31.2 DEGREES REMARK 500 SER A 154 C - N - CA ANGL. DEV. = 18.2 DEGREES REMARK 500 GLU B 1 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 GLU B 1 N - CA - C ANGL. DEV. = -23.6 DEGREES REMARK 500 ASP B 2 N - CA - C ANGL. DEV. = -26.6 DEGREES REMARK 500 PRO B 3 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 PRO B 4 N - CA - C ANGL. DEV. = 16.4 DEGREES REMARK 500 GLN B 51 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 CYS B 130 CA - CB - SG ANGL. DEV. = 11.1 DEGREES REMARK 500 PRO C 3 N - CA - C ANGL. DEV. = 25.4 DEGREES REMARK 500 PRO C 4 CA - N - CD ANGL. DEV. = -19.9 DEGREES REMARK 500 PRO C 4 N - CA - CB ANGL. DEV. = 13.0 DEGREES REMARK 500 PRO C 4 C - N - CD ANGL. DEV. = -34.4 DEGREES REMARK 500 CYS C 130 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 SER C 154 CB - CA - C ANGL. DEV. = -13.7 DEGREES REMARK 500 PRO D 3 CA - N - CD ANGL. DEV. = -16.5 DEGREES REMARK 500 PRO D 3 N - CD - CG ANGL. DEV. = 7.6 DEGREES REMARK 500 PRO D 3 C - N - CD ANGL. DEV. = -21.7 DEGREES REMARK 500 HIS D 42 CB - CG - CD2 ANGL. DEV. = 8.9 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 48.94 -63.92 REMARK 500 ALA A 5 94.95 74.82 REMARK 500 CYS A 6 -85.35 -81.96 REMARK 500 ALA A 92 98.61 -43.49 REMARK 500 HIS A 93 -15.48 -148.86 REMARK 500 ALA A 94 26.40 -146.54 REMARK 500 TYR A 111 43.55 -98.44 REMARK 500 PRO A 118 -30.18 -39.97 REMARK 500 GLN A 150 144.16 -179.28 REMARK 500 PRO A 151 72.96 -52.38 REMARK 500 PRO B 3 -101.88 6.60 REMARK 500 PRO B 4 -108.86 -42.15 REMARK 500 SER B 8 78.63 63.28 REMARK 500 ASP B 68 163.97 174.17 REMARK 500 HIS B 93 -18.19 -142.54 REMARK 500 TYR B 111 44.95 -99.45 REMARK 500 TRP B 166 134.67 -35.99 REMARK 500 PRO C 3 -35.04 11.93 REMARK 500 SER C 8 30.32 -156.32 REMARK 500 ASP C 68 168.28 169.95 REMARK 500 HIS C 93 -19.23 -141.87 REMARK 500 ASN C 113 57.14 -115.67 REMARK 500 PRO C 117 153.59 -48.56 REMARK 500 PRO C 151 77.16 -64.74 REMARK 500 PRO D 3 -147.68 -94.02 REMARK 500 PRO D 4 -82.63 -64.26 REMARK 500 ALA D 5 31.38 75.11 REMARK 500 ASP D 68 176.13 176.84 REMARK 500 MET D 108 114.76 -39.69 REMARK 500 ASN D 140 31.23 -97.84 REMARK 500 PRO D 151 91.25 -65.20 REMARK 500 ARG D 170 108.78 -173.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 153 27.21 REMARK 500 GLU B 1 10.95 REMARK 500 PRO C 3 -17.37 REMARK 500 SER C 154 12.15 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YCK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PEPTIDOGLYCAN RECOGNITION REMARK 900 PROTEIN (PGRP-S)
DBREF 2R90 A 1 171 UNP Q9GK12 PGRP_CAMDR 23 193 DBREF 2R90 B 1 171 UNP Q9GK12 PGRP_CAMDR 23 193 DBREF 2R90 C 1 171 UNP Q9GK12 PGRP_CAMDR 23 193 DBREF 2R90 D 1 171 UNP Q9GK12 PGRP_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
FORMUL 5 HOH *166(H2 O)
HELIX 1 1 ALA A 47 ASN A 63 1 17 HELIX 2 2 PRO A 117 GLY A 135 1 19 HELIX 3 3 HIS A 146 GLN A 150 1 5 HELIX 4 4 GLY A 156 GLN A 164 1 9 HELIX 5 5 PRO B 11 ARG B 16 1 6 HELIX 6 6 THR B 45 ARG B 62 1 18 HELIX 7 7 ALA B 94 ASN B 99 1 6 HELIX 8 8 PRO B 117 LEU B 134 1 18 HELIX 9 9 HIS B 146 GLN B 150 1 5 HELIX 10 10 GLY B 156 TRP B 166 1 11 HELIX 11 11 THR C 45 ASN C 63 1 19 HELIX 12 12 TRP C 98 PRO C 100 5 3 HELIX 13 13 PRO C 117 LEU C 134 1 18 HELIX 14 14 ARG C 147 VAL C 149 5 3 HELIX 15 15 GLY C 156 GLN C 164 1 9 HELIX 16 16 ARG D 12 ARG D 16 5 5 HELIX 17 17 THR D 45 ARG D 62 1 18 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 ARG D 147 VAL D 149 5 3 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 PHE A 73 SHEET 5 A 6 VAL A 30 HIS A 37 1 N VAL A 34 O ILE A 103 SHEET 6 A 6 LEU A 137 GLY A 145 1 O LYS A 144 N VAL A 33 SHEET 1 B 6 ILE B 9 VAL B 10 0 SHEET 2 B 6 VAL B 81 GLU B 83 1 O VAL B 81 N VAL B 10 SHEET 3 B 6 PHE B 73 ILE B 75 -1 N LEU B 74 O TYR B 82 SHEET 4 B 6 SER B 102 PHE B 107 1 O SER B 106 N ILE B 75 SHEET 5 B 6 VAL B 30 HIS B 37 1 N VAL B 34 O ILE B 103 SHEET 6 B 6 LEU B 137 GLY B 145 1 O GLU B 142 N ARG B 31 SHEET 1 C 5 VAL C 81 GLU C 83 0 SHEET 2 C 5 PHE C 73 ILE C 75 -1 N LEU C 74 O TYR C 82 SHEET 3 C 5 SER C 102 PHE C 107 1 O SER C 106 N ILE C 75 SHEET 4 C 5 VAL C 30 HIS C 37 1 N VAL C 34 O ILE C 103 SHEET 5 C 5 LEU C 137 GLY C 145 1 O GLU C 142 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 SER D 36 O ILE D 105 SHEET 6 D 6 LEU D 137 GLY D 145 1 O ARG D 138 N VAL D 30
SSBOND 1 CYS A 6 CYS A 130 1555 1555 1.78 SSBOND 2 CYS A 22 CYS A 67 1555 1555 2.03 SSBOND 3 CYS A 43 CYS A 49 1555 1555 2.03 SSBOND 4 CYS B 6 CYS B 130 1555 1555 2.05 SSBOND 5 CYS B 22 CYS B 67 1555 1555 2.03 SSBOND 6 CYS B 43 CYS B 49 1555 1555 2.03 SSBOND 7 CYS C 6 CYS C 130 1555 1555 2.01 SSBOND 8 CYS C 22 CYS C 67 1555 1555 2.03 SSBOND 9 CYS C 43 CYS C 49 1555 1555 2.03 SSBOND 10 CYS D 6 CYS D 130 1555 1555 2.03 SSBOND 11 CYS D 22 CYS D 67 1555 1555 2.03 SSBOND 12 CYS D 43 CYS D 49 1555 1555 2.03
CISPEP 1 ARG A 28 PRO A 29 0 5.33 CISPEP 2 SER A 154 PRO A 155 0 6.83 CISPEP 3 ARG B 28 PRO B 29 0 5.26 CISPEP 4 SER B 154 PRO B 155 0 -4.48 CISPEP 5 ARG C 28 PRO C 29 0 7.75 CISPEP 6 SER C 154 PRO C 155 0 2.31 CISPEP 7 ARG D 28 PRO D 29 0 -0.10 CISPEP 8 SER D 154 PRO D 155 0 0.31
CRYST1 89.849 102.370 164.111 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 0.011130 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009768 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006093 0.00000