HEADER ANTIBIOTIC, ANTIMICROBIAL PROTEIN 03-AUG-12 4GF9 TITLE STRUCTURAL INSIGHTS INTO THE DUAL STRATEGY OF RECOGNITION OF TITLE 2 PEPTIDOGLYCAN RECOGNITION PROTEIN, PGRP-S: TERNARY COMPLEX OF PGRP-S TITLE 3 WITH LPS AND FATTY ACID 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: CAMEL,DROMEDARIES,DROMEDARY,ONE-HUMPED CAMEL; SOURCE 4 ORGANISM_TAXID: 9838; SOURCE 5 STRAIN: CAMELUS DROMEDARIUS KEYWDS PEPTIDOGLYCAN BINDING, IMMUNE RESPONSE, SECRETED, ANTIMICROBIAL, KEYWDS 2 PGRP, ANTIBIOTIC, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.SHARMA,D.DUBE,M.SINHA,S.YADAV,P.KAUR,S.SHARMA,T.P.SINGH REVDAT 3 13-SEP-23 4GF9 1 REMARK REVDAT 2 15-MAY-13 4GF9 1 JRNL REVDAT 1 26-SEP-12 4GF9 0 JRNL AUTH P.SHARMA,D.DUBE,M.SINHA,S.YADAV,P.KAUR,S.SHARMA,T.P.SINGH JRNL TITL STRUCTURAL INSIGHTS INTO THE DUAL STRATEGY OF RECOGNITION BY JRNL TITL 2 PEPTIDOGLYCAN RECOGNITION PROTEIN, PGRP-S: STRUCTURE OF THE JRNL TITL 3 TERNARY COMPLEX OF PGRP-S WITH LIPOPOLYSACCHARIDE AND JRNL TITL 4 STEARIC ACID. JRNL REF PLOS ONE V. 8 53756 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23326499 JRNL DOI 10.1371/JOURNAL.PONE.0053756 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 17573 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 + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 950 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1259 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5344 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.73000 REMARK 3 B22 (A**2) : -4.29000 REMARK 3 B33 (A**2) : 3.56000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.432 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.337 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.582 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5575 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7591 ; 1.957 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 680 ; 7.963 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 268 ;37.758 ;22.090 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 816 ;21.190 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 64 ;17.992 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 783 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4381 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3399 ; 0.663 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5455 ; 1.222 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2176 ; 1.628 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2136 ; 2.760 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 171 REMARK 3 ORIGIN FOR THE GROUP (A): -22.4217 -37.0611 -45.4953 REMARK 3 T TENSOR REMARK 3 T11: 0.1596 T22: 0.1825 REMARK 3 T33: 0.4290 T12: -0.0640 REMARK 3 T13: -0.2160 T23: 0.1877 REMARK 3 L TENSOR REMARK 3 L11: 2.7410 L22: 1.7310 REMARK 3 L33: 4.9031 L12: -0.1042 REMARK 3 L13: -0.7368 L23: 0.2845 REMARK 3 S TENSOR REMARK 3 S11: -0.5294 S12: 0.1491 S13: 0.4854 REMARK 3 S21: 0.0109 S22: -0.3058 S23: 0.0141 REMARK 3 S31: -0.3168 S32: 0.1337 S33: 0.8353 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 171 REMARK 3 ORIGIN FOR THE GROUP (A): -36.1322 -15.2583 -60.6227 REMARK 3 T TENSOR REMARK 3 T11: 0.4433 T22: 0.2107 REMARK 3 T33: 0.1277 T12: -0.1289 REMARK 3 T13: -0.2075 T23: 0.1039 REMARK 3 L TENSOR REMARK 3 L11: 2.8853 L22: 6.7808 REMARK 3 L33: 1.0127 L12: 0.3908 REMARK 3 L13: 0.0093 L23: 0.0727 REMARK 3 S TENSOR REMARK 3 S11: 0.3031 S12: -0.0161 S13: -0.2326 REMARK 3 S21: 1.0522 S22: -0.4053 S23: -0.6745 REMARK 3 S31: -0.1501 S32: -0.0841 S33: 0.1022 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 171 REMARK 3 ORIGIN FOR THE GROUP (A): -27.1416 -38.2239 -8.7511 REMARK 3 T TENSOR REMARK 3 T11: 0.1501 T22: 0.1201 REMARK 3 T33: 0.4173 T12: 0.0904 REMARK 3 T13: -0.2017 T23: -0.2025 REMARK 3 L TENSOR REMARK 3 L11: 0.5056 L22: 2.4005 REMARK 3 L33: 2.3405 L12: 0.1842 REMARK 3 L13: 0.1541 L23: -0.0248 REMARK 3 S TENSOR REMARK 3 S11: -0.1564 S12: 0.0273 S13: 0.0693 REMARK 3 S21: -0.0563 S22: -0.2025 S23: 0.4682 REMARK 3 S31: -0.2457 S32: -0.1240 S33: 0.3589 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 171 REMARK 3 RESIDUE RANGE : D 201 D 201 REMARK 3 ORIGIN FOR THE GROUP (A): -36.7956 -12.4286 -18.2023 REMARK 3 T TENSOR REMARK 3 T11: 0.2652 T22: 0.2450 REMARK 3 T33: 0.3384 T12: 0.1469 REMARK 3 T13: -0.1298 T23: -0.1661 REMARK 3 L TENSOR REMARK 3 L11: 3.1983 L22: 6.0252 REMARK 3 L33: 2.3083 L12: 1.5242 REMARK 3 L13: -0.4655 L23: -0.1895 REMARK 3 S TENSOR REMARK 3 S11: -0.0723 S12: 0.3236 S13: -0.7834 REMARK 3 S21: 0.7474 S22: 0.2626 S23: -1.0319 REMARK 3 S31: -0.0585 S32: -0.0243 S33: -0.1903 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4GF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.8 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) : 0.97 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 : 17573 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 33.9000 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) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28900 REMARK 200 FOR SHELL : 4.300 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: PDB ENTRY 3C2X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% GLYCEROL, 6% PEG3350, PH 7.8, REMARK 280 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 44.81000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.94000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 81.65650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.81000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.94000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 81.65650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.81000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.94000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 81.65650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.81000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.94000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 81.65650 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: 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 ASN C 99 CB - CG - OD1 ANGL. DEV. = -12.3 DEGREES REMARK 500 PRO D 4 C - N - CD ANGL. DEV. = -20.1 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 ALA A 5 -157.42 -107.25 REMARK 500 CYS A 6 -46.76 -142.79 REMARK 500 ALA A 39 41.38 38.39 REMARK 500 ASP A 68 176.27 176.69 REMARK 500 ALA A 94 24.76 -145.19 REMARK 500 ASN A 140 36.80 -90.15 REMARK 500 HIS A 168 3.94 -154.02 REMARK 500 ASP B 2 -47.97 -138.55 REMARK 500 ALA B 5 -159.51 -161.61 REMARK 500 ARG B 23 -1.55 -143.76 REMARK 500 ALA B 94 30.40 -142.51 REMARK 500 PRO B 155 30.86 -98.32 REMARK 500 ALA C 5 -69.86 -166.73 REMARK 500 CYS C 6 -95.36 -124.47 REMARK 500 GLU C 83 109.86 -57.18 REMARK 500 HIS C 93 2.08 -152.08 REMARK 500 ALA C 94 19.42 -157.02 REMARK 500 ASP D 2 4.96 83.70 REMARK 500 PRO D 4 -130.85 50.74 REMARK 500 CYS D 6 -68.20 -107.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS D 6 GLY D 7 -140.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE STE B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LP5 C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 201 DBREF 4GF9 A 1 171 UNP Q9GK12 PGRP1_CAMDR 23 193 DBREF 4GF9 B 1 171 UNP Q9GK12 PGRP1_CAMDR 23 193 DBREF 4GF9 C 1 171 UNP Q9GK12 PGRP1_CAMDR 23 193 DBREF 4GF9 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 STE B 201 20 HET LP5 C 501 48 HET GOL D 201 6 HETNAM STE STEARIC ACID 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 GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 STE C18 H36 O2 FORMUL 6 LP5 C34 H66 N O12 P FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *255(H2 O) HELIX 1 1 THR A 45 ASN A 63 1 19 HELIX 2 2 ALA A 94 ASN A 99 1 6 HELIX 3 3 PRO A 117 LEU A 134 1 18 HELIX 4 4 ARG A 147 VAL A 149 5 3 HELIX 5 5 GLY A 156 GLN A 164 1 9 HELIX 6 6 PRO B 11 ARG B 16 5 6 HELIX 7 7 ALA B 47 ASN B 63 1 17 HELIX 8 8 ALA B 94 ASN B 99 1 6 HELIX 9 9 PRO B 117 ALA B 133 1 17 HELIX 10 10 HIS B 146 GLN B 150 1 5 HELIX 11 11 GLY B 156 THR B 165 1 10 HELIX 12 12 PRO C 11 TRP C 15 5 5 HELIX 13 13 THR C 45 ARG C 62 1 18 HELIX 14 14 TRP C 98 PRO C 100 5 3 HELIX 15 15 PRO C 117 LEU C 134 1 18 HELIX 16 16 HIS C 146 GLN C 150 1 5 HELIX 17 17 GLY C 156 GLN C 164 1 9 HELIX 18 18 PRO D 11 ARG D 16 1 6 HELIX 19 19 THR D 45 ARG D 62 1 18 HELIX 20 20 ALA D 94 ASN D 99 1 6 HELIX 21 21 PRO D 117 LEU D 134 1 18 HELIX 22 22 HIS D 146 GLN D 150 1 5 HELIX 23 23 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 GLU A 83 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 SER A 36 O PHE A 107 SHEET 6 A 6 LEU A 137 GLY A 145 1 O GLU A 142 N ARG A 31 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 ILE B 103 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 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 GLY C 104 N PHE C 73 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 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 2.04 SSBOND 2 CYS A 22 CYS A 67 1555 1555 2.06 SSBOND 3 CYS A 43 CYS A 49 1555 1555 2.08 SSBOND 4 CYS B 6 CYS B 130 1555 1555 2.04 SSBOND 5 CYS B 22 CYS B 67 1555 1555 2.05 SSBOND 6 CYS B 43 CYS B 49 1555 1555 2.05 SSBOND 7 CYS C 6 CYS C 130 1555 1555 2.01 SSBOND 8 CYS C 22 CYS C 67 1555 1555 2.06 SSBOND 9 CYS C 43 CYS C 49 1555 1555 2.05 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 2.06 CISPEP 1 ALA A 5 CYS A 6 0 12.37 CISPEP 2 ARG A 28 PRO A 29 0 1.87 CISPEP 3 SER A 154 PRO A 155 0 18.12 CISPEP 4 ALA B 5 CYS B 6 0 11.65 CISPEP 5 ARG B 28 PRO B 29 0 8.83 CISPEP 6 SER B 154 PRO B 155 0 6.25 CISPEP 7 PRO C 4 ALA C 5 0 -2.19 CISPEP 8 ARG C 28 PRO C 29 0 2.83 CISPEP 9 SER C 154 PRO C 155 0 10.84 CISPEP 10 PRO D 4 ALA D 5 0 0.68 CISPEP 11 ARG D 28 PRO D 29 0 2.30 CISPEP 12 SER D 154 PRO D 155 0 13.61 SITE 1 AC1 7 ASN A 126 ALA A 129 PRO B 4 ALA B 5 SITE 2 AC1 7 CYS B 6 ARG D 31 ARG D 138 SITE 1 AC2 21 ASN A 140 LEU C 64 ALA C 92 HIS C 93 SITE 2 AC2 21 ALA C 94 GLY C 95 PRO C 96 ASN C 99 SITE 3 AC2 21 GLN C 150 PRO C 151 HOH C 627 ALA D 94 SITE 4 AC2 21 GLY D 95 PRO D 96 THR D 97 TRP D 98 SITE 5 AC2 21 ASN D 99 LYS D 144 VAL D 149 GLN D 150 SITE 6 AC2 21 PRO D 151 SITE 1 AC3 6 PRO C 151 THR C 152 HIS D 37 ALA D 39 SITE 2 AC3 6 TYR D 71 HIS D 146 CRYST1 89.620 101.880 163.313 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 0.011158 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006123 0.00000