PDB Short entry for 2BSD HEADER RECEPTOR 20-MAY-05 2BSD TITLE STRUCTURE OF LACTOCOCCAL BACTERIOPHAGE P2 RECEPTOR BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR BINDING PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P2; SOURCE 3 ORGANISM_TAXID: 10679; SOURCE 4 STRAIN: LM0230; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS LACTOCOCCUS LACTIS, PHAGE, LLAMA VHH, RECEPTOR BINDING PROTEIN, KEYWDS 2 RECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR S.SPINELLI,A.DESMYTER,C.T.VERRIPS,H.J.W.DEHAARD,S.MOINEAU,C.CAMBILLAU REVDAT 6 24-JAN-18 2BSD 1 SOURCE REVDAT 5 13-JUL-11 2BSD 1 VERSN REVDAT 4 24-FEB-09 2BSD 1 VERSN REVDAT 3 11-JAN-06 2BSD 1 JRNL REVDAT 2 24-NOV-05 2BSD 1 JRNL REVDAT 1 02-NOV-05 2BSD 0 JRNL AUTH S.SPINELLI,A.DESMYTER,C.T.VERRIPS,H.J.W.DEHAARD,S.MOINEAU, JRNL AUTH 2 C.CAMBILLAU JRNL TITL LACTOCOCCAL BACTERIOPHAGE P2 RECEPTOR-BINDING PROTEIN JRNL TITL 2 STRUCTURE SUGGESTS A COMMON ANCESTOR GENE WITH BACTERIAL AND JRNL TITL 3 MAMMALIAN VIRUSES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 85 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16327804 JRNL DOI 10.1038/NSMB1029 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 48171 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1256 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3431 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5820 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 0.80000 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): 0.247 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.203 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.158 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5928 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8067 ; 1.148 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 756 ; 6.897 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 945 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4458 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2198 ; 0.189 ; 0.200 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): 168 ; 0.106 ; 0.200 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): 22 ; 0.204 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.068 ; 0.200 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): 3759 ; 0.420 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6105 ; 0.849 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2169 ; 1.369 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1962 ; 2.294 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 30 A 230 4 REMARK 3 1 B 30 B 230 4 REMARK 3 1 C 30 C 230 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1515 ; 0.13 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 1515 ; 0.15 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 C (A): 1515 ; 0.14 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1515 ; 0.41 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1515 ; 0.40 ; 2.00 REMARK 3 MEDIUM THERMAL 1 C (A**2): 1515 ; 0.42 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 2 A 264 REMARK 3 ORIGIN FOR THE GROUP (A): 59.0770 34.1590 32.4720 REMARK 3 T TENSOR REMARK 3 T11: 0.0014 T22: 0.0561 REMARK 3 T33: 0.0845 T12: 0.0005 REMARK 3 T13: 0.0095 T23: -0.0280 REMARK 3 L TENSOR REMARK 3 L11: 0.2010 L22: 1.0223 REMARK 3 L33: 0.6755 L12: -0.0037 REMARK 3 L13: 0.0689 L23: -0.5539 REMARK 3 S TENSOR REMARK 3 S11: 0.0230 S12: -0.0113 S13: 0.0277 REMARK 3 S21: 0.1003 S22: -0.0096 S23: 0.0463 REMARK 3 S31: -0.0531 S32: 0.0022 S33: -0.0134 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 2 B 264 REMARK 3 ORIGIN FOR THE GROUP (A): 71.4550 32.6080 16.9340 REMARK 3 T TENSOR REMARK 3 T11: 0.1057 T22: 0.0821 REMARK 3 T33: 0.0631 T12: -0.0262 REMARK 3 T13: 0.0305 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.9517 L22: 0.7506 REMARK 3 L33: 1.0696 L12: -0.6889 REMARK 3 L13: 0.6339 L23: -0.6065 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.1770 S13: 0.0303 REMARK 3 S21: -0.0754 S22: -0.0977 S23: -0.0847 REMARK 3 S31: -0.0352 S32: 0.1668 S33: 0.0653 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 2 C 264 REMARK 3 ORIGIN FOR THE GROUP (A): 54.8730 23.1560 16.5460 REMARK 3 T TENSOR REMARK 3 T11: 0.0426 T22: 0.1461 REMARK 3 T33: 0.0421 T12: 0.0032 REMARK 3 T13: -0.0145 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.4808 L22: 2.0819 REMARK 3 L33: 0.0431 L12: -0.5784 REMARK 3 L13: 0.0470 L23: -0.2068 REMARK 3 S TENSOR REMARK 3 S11: 0.0253 S12: 0.0236 S13: -0.0723 REMARK 3 S21: -0.1818 S22: -0.0144 S23: 0.0877 REMARK 3 S31: 0.0366 S32: -0.0416 S33: -0.0109 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2BSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1290024146. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48171 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE/RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A VOLUME OF 1 MICROL OF PROTEIN 6 TO 9 REMARK 280 MG/ML) WAS MIXED WITH 1 MICROL OF RESERVOIR SOLUTION CONTAINING REMARK 280 0.85-1.1 M AMMONIUM SULPHATE IN 0.1 M MES PH 6.5. CRYSTALS WERE REMARK 280 IMPROVED BY MICROSEEDING., PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 38.05400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.74550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.12500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.74550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.05400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.12500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 1 REMARK 465 SER A 10 REMARK 465 PRO A 11 REMARK 465 ASN A 12 REMARK 465 SER A 13 REMARK 465 THR A 14 REMARK 465 GLU A 15 REMARK 465 PHE A 16 REMARK 465 PRO A 17 REMARK 465 VAL A 18 REMARK 465 MET B 1 REMARK 465 SER B 10 REMARK 465 PRO B 11 REMARK 465 ASN B 12 REMARK 465 SER B 13 REMARK 465 THR B 14 REMARK 465 GLU B 15 REMARK 465 PHE B 16 REMARK 465 PRO B 17 REMARK 465 VAL B 18 REMARK 465 MET C 1 REMARK 465 SER C 10 REMARK 465 PRO C 11 REMARK 465 ASN C 12 REMARK 465 SER C 13 REMARK 465 THR C 14 REMARK 465 GLU C 15 REMARK 465 PHE C 16 REMARK 465 PRO C 17 REMARK 465 VAL C 18 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN C 177 NH1 ARG C 189 2.13 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 50 -137.47 47.33 REMARK 500 ASP A 146 -83.96 -94.67 REMARK 500 ASP A 184 -57.56 -141.32 REMARK 500 ASP A 249 -155.62 -83.08 REMARK 500 PHE B 6 -61.23 -121.40 REMARK 500 ALA B 50 -141.57 42.56 REMARK 500 LEU B 51 54.01 -90.78 REMARK 500 SER B 129 -158.28 -95.56 REMARK 500 ASP B 146 -78.55 -102.57 REMARK 500 ASP B 184 -63.91 -149.86 REMARK 500 ASP B 249 -156.52 -76.67 REMARK 500 ASP C 34 -169.20 -106.85 REMARK 500 ALA C 50 -135.69 46.07 REMARK 500 SER C 129 -159.07 -97.40 REMARK 500 ASP C 146 -83.93 -96.57 REMARK 500 ASP C 184 -58.53 -151.89 REMARK 500 ASP C 249 -154.59 -81.24 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 PHE A 8 PHE A 9 139.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BSE RELATED DB: PDB REMARK 900 STRUCTURE OF LACTOCOCCAL BACTERIOPHAGE P2 RECEPTOR BINDING PROTEIN REMARK 900 IN COMPLEX WITH A LLAMA VHH DOMAIN DBREF 2BSD A 1 264 UNP Q71AW2 Q71AW2_9CAUD 1 264 DBREF 2BSD B 1 264 UNP Q71AW2 Q71AW2_9CAUD 1 264 DBREF 2BSD C 1 264 UNP Q71AW2 Q71AW2_9CAUD 1 264 SEQRES 1 A 264 MET THR ILE LYS ASN PHE THR PHE PHE SER PRO ASN SER SEQRES 2 A 264 THR GLU PHE PRO VAL GLY SER ASN ASN ASP GLY LYS LEU SEQRES 3 A 264 TYR MET MET LEU THR GLY MET ASP TYR ARG THR ILE ARG SEQRES 4 A 264 ARG LYS ASP TRP SER SER PRO LEU ASN THR ALA LEU ASN SEQRES 5 A 264 VAL GLN TYR THR ASN THR SER ILE ILE ALA GLY GLY ARG SEQRES 6 A 264 TYR PHE GLU LEU LEU ASN GLU THR VAL ALA LEU LYS GLY SEQRES 7 A 264 ASP SER VAL ASN TYR ILE HIS ALA ASN ILE ASP LEU THR SEQRES 8 A 264 GLN THR ALA ASN PRO VAL SER LEU SER ALA GLU THR ALA SEQRES 9 A 264 ASN ASN SER ASN GLY VAL ASP ILE ASN ASN GLY SER GLY SEQRES 10 A 264 VAL LEU LYS VAL CYS PHE ASP ILE VAL THR THR SER GLY SEQRES 11 A 264 THR GLY VAL THR SER THR LYS PRO ILE VAL GLN THR SER SEQRES 12 A 264 THR LEU ASP SER ILE SER VAL ASN ASP MET THR VAL SER SEQRES 13 A 264 GLY SER ILE ASP VAL PRO VAL GLN THR LEU THR VAL GLU SEQRES 14 A 264 ALA GLY ASN GLY LEU GLN LEU GLN LEU THR LYS LYS ASN SEQRES 15 A 264 ASN ASP LEU VAL ILE VAL ARG PHE PHE GLY SER VAL SER SEQRES 16 A 264 ASN ILE GLN LYS GLY TRP ASN MET SER GLY THR TRP VAL SEQRES 17 A 264 ASP ARG PRO PHE ARG PRO ALA ALA VAL GLN SER LEU VAL SEQRES 18 A 264 GLY HIS PHE ALA GLY ARG ASP THR SER PHE HIS ILE ASP SEQRES 19 A 264 ILE ASN PRO ASN GLY SER ILE THR TRP TRP GLY ALA ASN SEQRES 20 A 264 ILE ASP LYS THR PRO ILE ALA THR ARG GLY ASN GLY SER SEQRES 21 A 264 TYR PHE ILE LYS SEQRES 1 B 264 MET THR ILE LYS ASN PHE THR PHE PHE SER PRO ASN SER SEQRES 2 B 264 THR GLU PHE PRO VAL GLY SER ASN ASN ASP GLY LYS LEU SEQRES 3 B 264 TYR MET MET LEU THR GLY MET ASP TYR ARG THR ILE ARG SEQRES 4 B 264 ARG LYS ASP TRP SER SER PRO LEU ASN THR ALA LEU ASN SEQRES 5 B 264 VAL GLN TYR THR ASN THR SER ILE ILE ALA GLY GLY ARG SEQRES 6 B 264 TYR PHE GLU LEU LEU ASN GLU THR VAL ALA LEU LYS GLY SEQRES 7 B 264 ASP SER VAL ASN TYR ILE HIS ALA ASN ILE ASP LEU THR SEQRES 8 B 264 GLN THR ALA ASN PRO VAL SER LEU SER ALA GLU THR ALA SEQRES 9 B 264 ASN ASN SER ASN GLY VAL ASP ILE ASN ASN GLY SER GLY SEQRES 10 B 264 VAL LEU LYS VAL CYS PHE ASP ILE VAL THR THR SER GLY SEQRES 11 B 264 THR GLY VAL THR SER THR LYS PRO ILE VAL GLN THR SER SEQRES 12 B 264 THR LEU ASP SER ILE SER VAL ASN ASP MET THR VAL SER SEQRES 13 B 264 GLY SER ILE ASP VAL PRO VAL GLN THR LEU THR VAL GLU SEQRES 14 B 264 ALA GLY ASN GLY LEU GLN LEU GLN LEU THR LYS LYS ASN SEQRES 15 B 264 ASN ASP LEU VAL ILE VAL ARG PHE PHE GLY SER VAL SER SEQRES 16 B 264 ASN ILE GLN LYS GLY TRP ASN MET SER GLY THR TRP VAL SEQRES 17 B 264 ASP ARG PRO PHE ARG PRO ALA ALA VAL GLN SER LEU VAL SEQRES 18 B 264 GLY HIS PHE ALA GLY ARG ASP THR SER PHE HIS ILE ASP SEQRES 19 B 264 ILE ASN PRO ASN GLY SER ILE THR TRP TRP GLY ALA ASN SEQRES 20 B 264 ILE ASP LYS THR PRO ILE ALA THR ARG GLY ASN GLY SER SEQRES 21 B 264 TYR PHE ILE LYS SEQRES 1 C 264 MET THR ILE LYS ASN PHE THR PHE PHE SER PRO ASN SER SEQRES 2 C 264 THR GLU PHE PRO VAL GLY SER ASN ASN ASP GLY LYS LEU SEQRES 3 C 264 TYR MET MET LEU THR GLY MET ASP TYR ARG THR ILE ARG SEQRES 4 C 264 ARG LYS ASP TRP SER SER PRO LEU ASN THR ALA LEU ASN SEQRES 5 C 264 VAL GLN TYR THR ASN THR SER ILE ILE ALA GLY GLY ARG SEQRES 6 C 264 TYR PHE GLU LEU LEU ASN GLU THR VAL ALA LEU LYS GLY SEQRES 7 C 264 ASP SER VAL ASN TYR ILE HIS ALA ASN ILE ASP LEU THR SEQRES 8 C 264 GLN THR ALA ASN PRO VAL SER LEU SER ALA GLU THR ALA SEQRES 9 C 264 ASN ASN SER ASN GLY VAL ASP ILE ASN ASN GLY SER GLY SEQRES 10 C 264 VAL LEU LYS VAL CYS PHE ASP ILE VAL THR THR SER GLY SEQRES 11 C 264 THR GLY VAL THR SER THR LYS PRO ILE VAL GLN THR SER SEQRES 12 C 264 THR LEU ASP SER ILE SER VAL ASN ASP MET THR VAL SER SEQRES 13 C 264 GLY SER ILE ASP VAL PRO VAL GLN THR LEU THR VAL GLU SEQRES 14 C 264 ALA GLY ASN GLY LEU GLN LEU GLN LEU THR LYS LYS ASN SEQRES 15 C 264 ASN ASP LEU VAL ILE VAL ARG PHE PHE GLY SER VAL SER SEQRES 16 C 264 ASN ILE GLN LYS GLY TRP ASN MET SER GLY THR TRP VAL SEQRES 17 C 264 ASP ARG PRO PHE ARG PRO ALA ALA VAL GLN SER LEU VAL SEQRES 18 C 264 GLY HIS PHE ALA GLY ARG ASP THR SER PHE HIS ILE ASP SEQRES 19 C 264 ILE ASN PRO ASN GLY SER ILE THR TRP TRP GLY ALA ASN SEQRES 20 C 264 ILE ASP LYS THR PRO ILE ALA THR ARG GLY ASN GLY SER SEQRES 21 C 264 TYR PHE ILE LYS FORMUL 4 HOH *215(H2 O) HELIX 1 1 GLY A 19 GLY A 32 1 14 HELIX 2 2 ASP A 209 ARG A 213 5 5 HELIX 3 3 GLY B 19 GLY B 32 1 14 HELIX 4 4 ASP B 209 ARG B 213 5 5 HELIX 5 5 GLY C 19 GLY C 32 1 14 HELIX 6 6 ASP C 209 ARG C 213 5 5 SHEET 1 AA 4 ILE A 3 ASN A 5 0 SHEET 2 AA 4 ARG A 65 LEU A 69 -1 O GLU A 68 N LYS A 4 SHEET 3 AA 4 ASN A 57 ALA A 62 -1 O THR A 58 N LEU A 69 SHEET 4 AA 4 ARG A 39 SER A 44 -1 O ARG A 39 N ILE A 61 SHEET 1 AB 3 LEU A 47 THR A 49 0 SHEET 2 AB 3 ASN A 52 TYR A 55 -1 O ASN A 52 N THR A 49 SHEET 3 AB 3 GLU A 72 ALA A 75 -1 O GLU A 72 N TYR A 55 SHEET 1 AC 4 VAL A 97 GLU A 102 0 SHEET 2 AC 4 VAL A 81 ILE A 88 -1 O TYR A 83 N GLU A 102 SHEET 3 AC 4 LEU A 119 THR A 128 -1 O LEU A 119 N ILE A 88 SHEET 4 AC 4 VAL A 133 PRO A 138 -1 N THR A 134 O THR A 127 SHEET 1 AD 4 THR A 142 THR A 144 0 SHEET 2 AD 4 THR C 142 VAL C 155 1 O SER C 147 N SER A 143 SHEET 3 AD 4 SER A 147 VAL A 150 1 O ILE A 148 N THR C 154 SHEET 4 AD 4 THR B 142 THR B 144 1 O SER B 143 N SER A 149 SHEET 1 AE 3 THR A 142 THR A 144 0 SHEET 2 AE 3 THR C 142 VAL C 155 1 O SER C 147 N SER A 143 SHEET 3 AE 3 SER B 147 ASP B 160 1 O SER B 147 N SER C 143 SHEET 1 AF 7 VAL A 163 GLY A 171 0 SHEET 2 AF 7 LEU A 174 LYS A 181 -1 O LEU A 174 N ALA A 170 SHEET 3 AF 7 LEU A 185 VAL A 194 -1 O LEU A 185 N LYS A 181 SHEET 4 AF 7 ILE A 253 PHE A 262 -1 O ILE A 253 N VAL A 194 SHEET 5 AF 7 GLN A 218 PHE A 224 -1 O HIS A 223 N ARG A 256 SHEET 6 AF 7 SER A 230 ILE A 235 -1 O PHE A 231 N GLY A 222 SHEET 7 AF 7 ILE A 241 TRP A 243 -1 O THR A 242 N ASP A 234 SHEET 1 BA 4 ILE B 3 ASN B 5 0 SHEET 2 BA 4 ARG B 65 LEU B 69 -1 O GLU B 68 N LYS B 4 SHEET 3 BA 4 ASN B 57 ALA B 62 -1 O THR B 58 N LEU B 69 SHEET 4 BA 4 ARG B 39 SER B 44 -1 O ARG B 39 N ILE B 61 SHEET 1 BB 2 ASN B 52 TYR B 55 0 SHEET 2 BB 2 GLU B 72 ALA B 75 -1 O GLU B 72 N TYR B 55 SHEET 1 BC 4 VAL B 97 GLU B 102 0 SHEET 2 BC 4 VAL B 81 ILE B 88 -1 O TYR B 83 N GLU B 102 SHEET 3 BC 4 LEU B 119 THR B 128 -1 O LEU B 119 N ILE B 88 SHEET 4 BC 4 VAL B 133 PRO B 138 -1 N THR B 134 O THR B 127 SHEET 1 BD 7 VAL B 163 GLY B 171 0 SHEET 2 BD 7 LEU B 174 LYS B 181 -1 O LEU B 174 N ALA B 170 SHEET 3 BD 7 LEU B 185 VAL B 194 -1 O LEU B 185 N LYS B 181 SHEET 4 BD 7 ILE B 253 PHE B 262 -1 O ILE B 253 N VAL B 194 SHEET 5 BD 7 GLN B 218 PHE B 224 -1 O HIS B 223 N ARG B 256 SHEET 6 BD 7 SER B 230 ILE B 235 -1 O PHE B 231 N GLY B 222 SHEET 7 BD 7 ILE B 241 TRP B 243 -1 O THR B 242 N ASP B 234 SHEET 1 CA 4 ILE C 3 ASN C 5 0 SHEET 2 CA 4 ARG C 65 ALA C 75 -1 O GLU C 68 N LYS C 4 SHEET 3 CA 4 ASN C 52 ALA C 62 -1 O VAL C 53 N VAL C 74 SHEET 4 CA 4 ARG C 39 ASP C 42 -1 O ARG C 39 N ILE C 61 SHEET 1 CB 4 ILE C 3 ASN C 5 0 SHEET 2 CB 4 ARG C 65 ALA C 75 -1 O GLU C 68 N LYS C 4 SHEET 3 CB 4 ASN C 52 ALA C 62 -1 O VAL C 53 N VAL C 74 SHEET 4 CB 4 LEU C 47 ASN C 48 -1 O LEU C 47 N GLN C 54 SHEET 1 CC 4 VAL C 97 GLU C 102 0 SHEET 2 CC 4 VAL C 81 ILE C 88 -1 O TYR C 83 N GLU C 102 SHEET 3 CC 4 LEU C 119 THR C 128 -1 O LEU C 119 N ILE C 88 SHEET 4 CC 4 VAL C 133 PRO C 138 -1 N THR C 134 O THR C 127 SHEET 1 CD 7 VAL C 163 GLY C 171 0 SHEET 2 CD 7 LEU C 174 LYS C 181 -1 O LEU C 174 N ALA C 170 SHEET 3 CD 7 LEU C 185 VAL C 194 -1 O LEU C 185 N LYS C 181 SHEET 4 CD 7 ILE C 253 PHE C 262 -1 O ILE C 253 N VAL C 194 SHEET 5 CD 7 GLN C 218 PHE C 224 -1 O HIS C 223 N ARG C 256 SHEET 6 CD 7 SER C 230 ILE C 235 -1 O PHE C 231 N GLY C 222 SHEET 7 CD 7 ILE C 241 TRP C 243 -1 O THR C 242 N ASP C 234 CRYST1 76.108 96.250 149.491 90.00 90.00 90.00 P 21 21 21 12 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 0.013139 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006689 0.00000