HEADER CELL ADHESION 17-JUN-12 4FMK TITLE CRYSTAL STRUCTURE OF MOUSE NECTIN-2 EXTRACELLULAR FRAGMENT D1-D2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLIOVIRUS RECEPTOR-RELATED PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN (D1-D2, UNP RESIDUES 32-250); COMPND 5 SYNONYM: NECTIN-2, HERPES VIRUS ENTRY MEDIATOR B, HERPESVIRUS ENTRY COMPND 6 MEDIATOR B, HVEB, MURINE HERPES VIRUS ENTRY PROTEIN B, MHVEB, COMPND 7 POLIOVIRUS RECEPTOR HOMOLOG; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PVRL2, MPH, PVR, PVS; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK 293F; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCEP4 KEYWDS IMMUNOGLOBULIN-LIKE DOMAIN, IG DOMAIN, VIRAL ENTRY RECEPTOR, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR O.J.HARRISON,J.BRASCH,L.SHAPIRO REVDAT 5 13-SEP-23 4FMK 1 HETSYN REVDAT 4 29-JUL-20 4FMK 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 26-SEP-12 4FMK 1 JRNL REVDAT 2 05-SEP-12 4FMK 1 JRNL REVDAT 1 22-AUG-12 4FMK 0 JRNL AUTH O.J.HARRISON,J.VENDOME,J.BRASCH,X.JIN,S.HONG,P.S.KATSAMBA, JRNL AUTH 2 G.AHLSEN,R.B.TROYANOVSKY,S.M.TROYANOVSKY,B.HONIG,L.SHAPIRO JRNL TITL NECTIN ECTODOMAIN STRUCTURES REVEAL A CANONICAL ADHESIVE JRNL TITL 2 INTERFACE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 906 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 22902367 JRNL DOI 10.1038/NSMB.2366 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14118 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 708 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) : 2.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 898 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.3720 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.5060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1717 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 135 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.63000 REMARK 3 B22 (A**2) : 4.63000 REMARK 3 B33 (A**2) : -6.95000 REMARK 3 B12 (A**2) : 2.32000 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): 0.328 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.262 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.225 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.933 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1902 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1294 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2612 ; 1.667 ; 2.035 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3100 ; 1.094 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 220 ; 6.311 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;37.712 ;21.951 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 272 ;17.677 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.521 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 325 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2011 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 385 ; 0.004 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 33 A 149 REMARK 3 ORIGIN FOR THE GROUP (A): -2.1263 -6.5942 12.4698 REMARK 3 T TENSOR REMARK 3 T11: 0.1830 T22: 0.1500 REMARK 3 T33: 0.1112 T12: 0.0071 REMARK 3 T13: -0.0421 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 3.6904 L22: 6.1190 REMARK 3 L33: 12.1248 L12: -0.4166 REMARK 3 L13: -3.5020 L23: -1.7158 REMARK 3 S TENSOR REMARK 3 S11: 0.1367 S12: 0.0601 S13: -0.3477 REMARK 3 S21: -0.1856 S22: 0.1807 S23: -0.1644 REMARK 3 S31: 0.2831 S32: 0.0080 S33: -0.3174 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 : A 150 A 253 REMARK 3 ORIGIN FOR THE GROUP (A): -25.7599 -26.6359 41.3354 REMARK 3 T TENSOR REMARK 3 T11: 0.3535 T22: 0.5670 REMARK 3 T33: 0.3846 T12: -0.0340 REMARK 3 T13: 0.0580 T23: 0.2914 REMARK 3 L TENSOR REMARK 3 L11: 4.9334 L22: 9.4149 REMARK 3 L33: 6.4137 L12: 3.6785 REMARK 3 L13: -2.2757 L23: -5.2491 REMARK 3 S TENSOR REMARK 3 S11: -0.0012 S12: 0.4302 S13: -0.2286 REMARK 3 S21: -0.4558 S22: 0.3360 S23: 0.4310 REMARK 3 S31: 0.6556 S32: -0.7015 S33: -0.3348 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 4FMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : BENT SINGLE SI(111) CRYSTAL REMARK 200 (HORIZONTAL FOCUSING AND REMARK 200 DEFLECTION) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14118 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54000 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3ALP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% W/V PEG6000, 0.05 M CADMIUM REMARK 280 SULFATE, 0.2 M SODIUM ACETATE, 0.1 M MES, PH 6.0, CRYOPROTECTANT: REMARK 280 15% 2R,3R-BUTANE-DI-OL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.20167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.40333 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 106.40333 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.20167 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: DIMERIC 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 350 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLN A 32 REMARK 465 HIS A 254 REMARK 465 HIS A 255 REMARK 465 HIS A 256 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 OE1 GLU A 161 CD CD A 312 4445 2.18 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 HIS A 55 CG HIS A 55 CD2 0.055 REMARK 500 ASP A 110 CB ASP A 110 CG 0.141 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 105 36.32 -78.15 REMARK 500 THR A 107 32.26 -142.30 REMARK 500 ILE A 164 152.72 -42.28 REMARK 500 PRO A 181 -173.91 -65.73 REMARK 500 LEU A 191 -175.56 -69.60 REMARK 500 PRO A 218 95.45 -66.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 312 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 156 NE2 REMARK 620 2 GLU A 158 OE2 64.2 REMARK 620 3 GLU A 158 OE1 112.8 48.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 313 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 223 OD2 REMARK 620 2 ASP A 223 OD1 57.7 REMARK 620 3 HIS A 252 ND1 107.8 72.4 REMARK 620 4 HOH A 418 O 76.9 130.7 146.5 REMARK 620 5 HOH A 419 O 153.5 148.2 84.6 80.1 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FMF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NECTIN-1 REMARK 900 RELATED ID: 4FN0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NECTIN-2, 2ND CRYSTAL FORM DBREF 4FMK A 32 250 UNP P32507 PVRL2_MOUSE 32 250 SEQADV 4FMK HIS A 251 UNP P32507 EXPRESSION TAG SEQADV 4FMK HIS A 252 UNP P32507 EXPRESSION TAG SEQADV 4FMK HIS A 253 UNP P32507 EXPRESSION TAG SEQADV 4FMK HIS A 254 UNP P32507 EXPRESSION TAG SEQADV 4FMK HIS A 255 UNP P32507 EXPRESSION TAG SEQADV 4FMK HIS A 256 UNP P32507 EXPRESSION TAG SEQRES 1 A 225 GLN ASP VAL ARG VAL ARG VAL LEU PRO GLU VAL ARG GLY SEQRES 2 A 225 ARG LEU GLY GLY THR VAL GLU LEU PRO CYS HIS LEU LEU SEQRES 3 A 225 PRO PRO THR THR GLU ARG VAL SER GLN VAL THR TRP GLN SEQRES 4 A 225 ARG LEU ASP GLY THR VAL VAL ALA ALA PHE HIS PRO SER SEQRES 5 A 225 PHE GLY VAL ASP PHE PRO ASN SER GLN PHE SER LYS ASP SEQRES 6 A 225 ARG LEU SER PHE VAL ARG ALA ARG PRO GLU THR ASN ALA SEQRES 7 A 225 ASP LEU ARG ASP ALA THR LEU ALA PHE ARG GLY LEU ARG SEQRES 8 A 225 VAL GLU ASP GLU GLY ASN TYR THR CYS GLU PHE ALA THR SEQRES 9 A 225 PHE PRO ASN GLY THR ARG ARG GLY VAL THR TRP LEU ARG SEQRES 10 A 225 VAL ILE ALA GLN PRO GLU ASN HIS ALA GLU ALA GLN GLU SEQRES 11 A 225 VAL THR ILE GLY PRO GLN SER VAL ALA VAL ALA ARG CYS SEQRES 12 A 225 VAL SER THR GLY GLY ARG PRO PRO ALA ARG ILE THR TRP SEQRES 13 A 225 ILE SER SER LEU GLY GLY GLU ALA LYS ASP THR GLN GLU SEQRES 14 A 225 PRO GLY ILE GLN ALA GLY THR VAL THR ILE ILE SER ARG SEQRES 15 A 225 TYR SER LEU VAL PRO VAL GLY ARG ALA ASP GLY VAL LYS SEQRES 16 A 225 VAL THR CYS ARG VAL GLU HIS GLU SER PHE GLU GLU PRO SEQRES 17 A 225 ILE LEU LEU PRO VAL THR LEU SER VAL ARG TYR HIS HIS SEQRES 18 A 225 HIS HIS HIS HIS MODRES 4FMK ASN A 128 ASN GLYCOSYLATION SITE MODRES 4FMK ASN A 138 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HET FUC B 6 10 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET FUC C 5 10 HET CD A 312 1 HET CD A 313 1 HET CD A 314 1 HET CD A 315 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CD CADMIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 2 MAN 3(C6 H12 O6) FORMUL 2 FUC 2(C6 H12 O5) FORMUL 4 CD 4(CD 2+) FORMUL 8 HOH *36(H2 O) HELIX 1 1 ARG A 122 GLU A 126 5 5 HELIX 2 2 VAL A 219 ASP A 223 5 5 SHEET 1 A 2 VAL A 36 ARG A 37 0 SHEET 2 A 2 HIS A 55 LEU A 56 -1 O HIS A 55 N ARG A 37 SHEET 1 B 6 GLU A 41 ARG A 45 0 SHEET 2 B 6 GLY A 139 ILE A 150 1 O ILE A 150 N GLY A 44 SHEET 3 B 6 GLY A 127 PHE A 136 -1 N CYS A 131 O GLY A 143 SHEET 4 B 6 ARG A 63 GLN A 70 -1 N SER A 65 O ALA A 134 SHEET 5 B 6 VAL A 76 HIS A 81 -1 O PHE A 80 N VAL A 67 SHEET 6 B 6 GLY A 85 ASP A 87 -1 O ASP A 87 N ALA A 79 SHEET 1 C 3 VAL A 50 LEU A 52 0 SHEET 2 C 3 LEU A 116 PHE A 118 -1 O LEU A 116 N LEU A 52 SHEET 3 C 3 LEU A 98 PHE A 100 -1 N SER A 99 O ALA A 117 SHEET 1 D 4 GLU A 154 ALA A 159 0 SHEET 2 D 4 VAL A 169 GLY A 179 -1 O VAL A 175 N HIS A 156 SHEET 3 D 4 VAL A 208 LEU A 216 -1 O TYR A 214 N ALA A 172 SHEET 4 D 4 GLU A 194 PRO A 201 -1 N GLU A 200 O THR A 209 SHEET 1 E 3 ARG A 184 ILE A 188 0 SHEET 2 E 3 LYS A 226 GLU A 232 -1 O ARG A 230 N THR A 186 SHEET 3 E 3 ILE A 240 THR A 245 -1 O VAL A 244 N VAL A 227 SSBOND 1 CYS A 54 CYS A 131 1555 1555 2.05 SSBOND 2 CYS A 174 CYS A 229 1555 1555 1.99 LINK ND2 ASN A 128 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 138 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O6 NAG B 1 C1 FUC B 6 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.45 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.45 LINK O6 BMA B 3 C1 MAN B 5 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O6 NAG C 1 C1 FUC C 5 1555 1555 1.46 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.44 LINK NE2 HIS A 156 CD CD A 312 1555 1555 2.58 LINK OE2 GLU A 158 CD CD A 312 1555 1555 2.62 LINK OE1 GLU A 158 CD CD A 312 1555 1555 2.69 LINK OD2 ASP A 223 CD CD A 313 1555 1555 2.22 LINK OD1 ASP A 223 CD CD A 313 1555 1555 2.29 LINK ND1 HIS A 251 CD CD A 315 1555 1555 2.53 LINK ND1 HIS A 252 CD CD A 313 1555 1555 2.19 LINK CD CD A 313 O HOH A 418 1555 1555 2.11 LINK CD CD A 313 O HOH A 419 1555 1555 1.87 CISPEP 1 PRO A 58 PRO A 59 0 -14.91 CISPEP 2 PHE A 136 PRO A 137 0 3.25 CISPEP 3 ARG A 180 PRO A 181 0 -2.25 CRYST1 68.666 68.666 159.605 90.00 90.00 120.00 P 31 1 2 6 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 0.014563 0.008408 0.000000 0.00000 SCALE2 0.000000 0.016816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006265 0.00000