HEADER CELL ADHESION 20-JUN-12 4FOM
TITLE CRYSTAL STRUCTURE OF HUMAN NECTIN-3 FULL ECTODOMAIN (D1-D3)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: POLIOVIRUS RECEPTOR-RELATED PROTEIN 3;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ECTODOMAIN (D1-D3, UNP RESIDUES 58-359);
COMPND 5 SYNONYM: NECTIN-3, CDW113;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PVRL3, PRR3;
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, CELL ADHESION
EXPDTA X-RAY DIFFRACTION
AUTHOR O.J.HARRISON,X.JIN,J.BRASCH,L.SHAPIRO
REVDAT 5 13-SEP-23 4FOM 1 HETSYN
REVDAT 4 29-JUL-20 4FOM 1 COMPND REMARK SEQADV HETNAM
REVDAT 4 2 1 LINK SITE ATOM
REVDAT 3 26-SEP-12 4FOM 1 JRNL
REVDAT 2 05-SEP-12 4FOM 1 JRNL
REVDAT 1 22-AUG-12 4FOM 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. 3.93 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) : 3.93
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 3 NUMBER OF REFLECTIONS : 11210
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) : 0.248
REMARK 3 R VALUE (WORKING SET) : 0.247
REMARK 3 FREE R VALUE : 0.279
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700
REMARK 3 FREE R VALUE TEST SET COUNT : 558
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) : 3.93
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.03
REMARK 3 REFLECTION IN BIN (WORKING SET) : 659
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.74
REMARK 3 BIN R VALUE (WORKING SET) : 0.3250
REMARK 3 BIN FREE R VALUE SET COUNT : 34
REMARK 3 BIN FREE R VALUE : 0.3740
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2342
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 246
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 170.5
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 4.45000
REMARK 3 B22 (A**2) : 4.45000
REMARK 3 B33 (A**2) : -6.68000
REMARK 3 B12 (A**2) : 2.23000
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): 1.721
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.538
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.467
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 62.326
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2656 ; 0.016 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): 1735 ; 0.004 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3628 ; 1.295 ; 2.041
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4206 ; 0.934 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 8.555 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;41.454 ;24.455
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 381 ;22.382 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;22.335 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.058 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2742 ; 0.011 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 488 ; 0.005 ; 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 : 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 58 A 168
REMARK 3 ORIGIN FOR THE GROUP (A): -38.0574 38.2624 -18.6403
REMARK 3 T TENSOR
REMARK 3 T11: 1.9288 T22: 0.3630
REMARK 3 T33: 2.2114 T12: 0.8083
REMARK 3 T13: 0.1545 T23: -0.0733
REMARK 3 L TENSOR
REMARK 3 L11: 23.7302 L22: 3.3393
REMARK 3 L33: 5.1183 L12: -8.4941
REMARK 3 L13: 1.7204 L23: -0.3595
REMARK 3 S TENSOR
REMARK 3 S11: -0.1647 S12: -0.4974 S13: -0.6993
REMARK 3 S21: 0.2556 S22: 0.1807 S23: 1.0239
REMARK 3 S31: -0.3135 S32: -0.3375 S33: -0.0160
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 169 A 266
REMARK 3 ORIGIN FOR THE GROUP (A): -1.7516 17.5426 -13.5384
REMARK 3 T TENSOR
REMARK 3 T11: 0.9577 T22: 0.3490
REMARK 3 T33: 0.5263 T12: -0.0074
REMARK 3 T13: 0.1391 T23: -0.1416
REMARK 3 L TENSOR
REMARK 3 L11: 10.9489 L22: 8.8400
REMARK 3 L33: 6.1239 L12: -8.4624
REMARK 3 L13: 5.1878 L23: -3.6662
REMARK 3 S TENSOR
REMARK 3 S11: -0.2099 S12: -0.9265 S13: 0.6322
REMARK 3 S21: 0.3906 S22: 0.1480 S23: 0.0974
REMARK 3 S31: -1.2822 S32: -0.1170 S33: 0.0619
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 : A 267 A 359
REMARK 3 ORIGIN FOR THE GROUP (A): 22.0198 -17.6716 0.5228
REMARK 3 T TENSOR
REMARK 3 T11: 0.7843 T22: 0.8690
REMARK 3 T33: 0.7482 T12: 0.4524
REMARK 3 T13: 0.0882 T23: 0.0939
REMARK 3 L TENSOR
REMARK 3 L11: 4.9135 L22: 12.1116
REMARK 3 L33: 15.0762 L12: -5.6370
REMARK 3 L13: 6.4061 L23: -9.3634
REMARK 3 S TENSOR
REMARK 3 S11: 0.2104 S12: -0.1544 S13: -0.4447
REMARK 3 S21: 0.2378 S22: -0.4041 S23: -0.5041
REMARK 3 S31: 1.3336 S32: 1.7918 S33: 0.1938
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 4FOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-12.
REMARK 100 THE DEPOSITION ID IS D_1000073160.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JUL-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.6
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 : 11776
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.930
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 (%) : 98.3
REMARK 200 DATA REDUNDANCY : 5.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.07000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.93
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.07
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : 6.10
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.61000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200
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 (%): 86.52
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 9.13
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 4.6 M AMMONIUM ACETATE, 0.1 M SODIUM
REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K, PH
REMARK 280 4.6
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
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 165.02867
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 82.51433
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 123.77150
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.25717
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 206.28583
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 165.02867
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 82.51433
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.25717
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 123.77150
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 206.28583
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, D, E
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 -65.93350
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 114.20017
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -41.25717
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 HIS A 360
REMARK 465 HIS A 361
REMARK 465 HIS A 362
REMARK 465 HIS A 363
REMARK 465 HIS A 364
REMARK 465 HIS A 365
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 OD1 ASN A 186 C1 NAG D 1 1.84
REMARK 500 ND2 ASN A 186 O5 NAG D 1 1.92
REMARK 500 CG ASN A 186 C1 NAG D 1 1.93
REMARK 500 O4 NAG C 1 C2 NAG C 2 2.05
REMARK 500 ND2 ASN A 222 O5 NAG E 1 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 ASN A 186 CG ASN A 186 ND2 -0.151
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 PHE A 153 CB - CA - C ANGL. DEV. = -13.1 DEGREES
REMARK 500 PRO A 154 N - CA - CB ANGL. DEV. = -16.6 DEGREES
REMARK 500 PRO A 154 N - CD - CG ANGL. DEV. = -16.2 DEGREES
REMARK 500 PRO A 154 N - CA - C ANGL. DEV. = 21.8 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 GLU A 81 83.46 -65.71
REMARK 500 ASN A 83 0.11 -58.18
REMARK 500 LYS A 97 -9.40 69.88
REMARK 500 TYR A 109 54.08 -107.92
REMARK 500 TYR A 117 1.35 -67.40
REMARK 500 ASN A 137 75.64 63.16
REMARK 500 LEU A 155 -37.76 -33.47
REMARK 500 ASN A 186 153.01 -43.71
REMARK 500 GLU A 187 139.08 -38.13
REMARK 500 ASP A 205 134.26 -174.50
REMARK 500 GLU A 214 153.84 175.34
REMARK 500 ASN A 222 -6.20 -55.19
REMARK 500 CYS A 291 32.42 -95.86
REMARK 500 ASN A 292 132.96 -35.54
REMARK 500 PHE A 300 -51.12 -122.69
REMARK 500 SER A 302 47.17 -145.03
REMARK 500 TRP A 304 61.16 -114.35
REMARK 500 ALA A 317 65.11 -116.40
REMARK 500 ASP A 319 -117.15 57.57
REMARK 500 PHE A 324 75.63 -116.13
REMARK 500 PRO A 327 150.25 -48.06
REMARK 500 TYR A 332 -6.35 84.51
REMARK 500 SER A 343 -38.05 -36.06
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4FMF RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN NECTIN-1 FULL ECTODOMAIN D1-D3
REMARK 900 RELATED ID: 4FMK RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF MURINE NECTIN-2 FRAGMENT D1-D2
REMARK 900 RELATED ID: 4FN0 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF MURINE NECTIN-2 FRAGMENT D1-D2, 2ND CRYSTAL
REMARK 900 FORM
REMARK 900 RELATED ID: 4FQP RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN NECTIN-LIKE 5 FULL ECTODOMAIN D1-D3
REMARK 900 RELATED ID: 4FRW RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN NECTIN-4 FRAGMENT D1-D2
REMARK 900 RELATED ID: 4FS0 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF MUTANT F136D OF MOUSE NECTIN-2 FRAGMENT D1-D2
DBREF 4FOM A 58 359 UNP Q9NQS3 PVRL3_HUMAN 58 359
SEQADV 4FOM HIS A 360 UNP Q9NQS3 EXPRESSION TAG
SEQADV 4FOM HIS A 361 UNP Q9NQS3 EXPRESSION TAG
SEQADV 4FOM HIS A 362 UNP Q9NQS3 EXPRESSION TAG
SEQADV 4FOM HIS A 363 UNP Q9NQS3 EXPRESSION TAG
SEQADV 4FOM HIS A 364 UNP Q9NQS3 EXPRESSION TAG
SEQADV 4FOM HIS A 365 UNP Q9NQS3 EXPRESSION TAG
SEQRES 1 A 308 GLY PRO ILE ILE VAL GLU PRO HIS VAL THR ALA VAL TRP
SEQRES 2 A 308 GLY LYS ASN VAL SER LEU LYS CYS LEU ILE GLU VAL ASN
SEQRES 3 A 308 GLU THR ILE THR GLN ILE SER TRP GLU LYS ILE HIS GLY
SEQRES 4 A 308 LYS SER SER GLN THR VAL ALA VAL HIS HIS PRO GLN TYR
SEQRES 5 A 308 GLY PHE SER VAL GLN GLY GLU TYR GLN GLY ARG VAL LEU
SEQRES 6 A 308 PHE LYS ASN TYR SER LEU ASN ASP ALA THR ILE THR LEU
SEQRES 7 A 308 HIS ASN ILE GLY PHE SER ASP SER GLY LYS TYR ILE CYS
SEQRES 8 A 308 LYS ALA VAL THR PHE PRO LEU GLY ASN ALA GLN SER SER
SEQRES 9 A 308 THR THR VAL THR VAL LEU VAL GLU PRO THR VAL SER LEU
SEQRES 10 A 308 ILE LYS GLY PRO ASP SER LEU ILE ASP GLY GLY ASN GLU
SEQRES 11 A 308 THR VAL ALA ALA ILE CYS ILE ALA ALA THR GLY LYS PRO
SEQRES 12 A 308 VAL ALA HIS ILE ASP TRP GLU GLY ASP LEU GLY GLU MET
SEQRES 13 A 308 GLU SER THR THR THR SER PHE PRO ASN GLU THR ALA THR
SEQRES 14 A 308 ILE ILE SER GLN TYR LYS LEU PHE PRO THR ARG PHE ALA
SEQRES 15 A 308 ARG GLY ARG ARG ILE THR CYS VAL VAL LYS HIS PRO ALA
SEQRES 16 A 308 LEU GLU LYS ASP ILE ARG TYR SER PHE ILE LEU ASP ILE
SEQRES 17 A 308 GLN TYR ALA PRO GLU VAL SER VAL THR GLY TYR ASP GLY
SEQRES 18 A 308 ASN TRP PHE VAL GLY ARG LYS GLY VAL ASN LEU LYS CYS
SEQRES 19 A 308 ASN ALA ASP ALA ASN PRO PRO PRO PHE LYS SER VAL TRP
SEQRES 20 A 308 SER ARG LEU ASP GLY GLN TRP PRO ASP GLY LEU LEU ALA
SEQRES 21 A 308 SER ASP ASN THR LEU HIS PHE VAL HIS PRO LEU THR PHE
SEQRES 22 A 308 ASN TYR SER GLY VAL TYR ILE CYS LYS VAL THR ASN SER
SEQRES 23 A 308 LEU GLY GLN ARG SER ASP GLN LYS VAL ILE TYR ILE SER
SEQRES 24 A 308 ASP PRO PRO HIS HIS HIS HIS HIS HIS
MODRES 4FOM ASN A 186 ASN GLYCOSYLATION SITE
MODRES 4FOM ASN A 73 ASN GLYCOSYLATION SITE
MODRES 4FOM ASN A 125 ASN GLYCOSYLATION SITE
MODRES 4FOM ASN A 331 ASN GLYCOSYLATION SITE
MODRES 4FOM ASN A 222 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 NAG C 1 14
HET NAG C 2 14
HET BMA C 3 11
HET NAG D 1 14
HET NAG D 2 14
HET BMA D 3 11
HET MAN D 4 11
HET MAN D 5 11
HET FUC D 6 10
HET NAG E 1 14
HET NAG E 2 14
HET BMA E 3 11
HET MAN E 4 11
HET MAN E 5 11
HET NAG A 420 14
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM BMA BETA-D-MANNOPYRANOSE
HETNAM MAN ALPHA-D-MANNOPYRANOSE
HETNAM FUC ALPHA-L-FUCOPYRANOSE
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 9(C8 H15 N O6)
FORMUL 2 BMA 4(C6 H12 O6)
FORMUL 2 MAN 6(C6 H12 O6)
FORMUL 4 FUC C6 H12 O5
HELIX 1 1 GLY A 139 SER A 143 5 5
HELIX 2 2 THR A 236 ARG A 240 5 5
SHEET 1 A 6 THR A 67 VAL A 69 0
SHEET 2 A 6 GLY A 156 LEU A 167 1 O LEU A 167 N ALA A 68
SHEET 3 A 6 GLY A 144 THR A 152 -1 N THR A 152 O GLY A 156
SHEET 4 A 6 ILE A 86 ILE A 94 -1 N GLU A 92 O ILE A 147
SHEET 5 A 6 SER A 99 HIS A 105 -1 O VAL A 102 N TRP A 91
SHEET 6 A 6 PHE A 111 VAL A 113 -1 O SER A 112 N VAL A 104
SHEET 1 B 3 VAL A 74 LEU A 76 0
SHEET 2 B 3 ILE A 133 LEU A 135 -1 O ILE A 133 N LEU A 76
SHEET 3 B 3 VAL A 121 PHE A 123 -1 N LEU A 122 O THR A 134
SHEET 1 C 4 THR A 171 LYS A 176 0
SHEET 2 C 4 THR A 188 GLY A 198 -1 O ILE A 194 N SER A 173
SHEET 3 C 4 ALA A 225 LEU A 233 -1 O TYR A 231 N ALA A 191
SHEET 4 C 4 SER A 215 SER A 219 -1 N THR A 218 O THR A 226
SHEET 1 D 3 HIS A 203 TRP A 206 0
SHEET 2 D 3 ARG A 243 LYS A 249 -1 O VAL A 247 N ASP A 205
SHEET 3 D 3 ILE A 257 ILE A 262 -1 O ILE A 257 N VAL A 248
SHEET 1 E 2 TYR A 267 VAL A 271 0
SHEET 2 E 2 ALA A 293 ASN A 296 -1 O ASN A 296 N TYR A 267
SHEET 1 F 2 TRP A 280 PHE A 281 0
SHEET 2 F 2 ILE A 355 SER A 356 1 O SER A 356 N TRP A 280
SHEET 1 G 2 ASN A 288 LYS A 290 0
SHEET 2 G 2 THR A 321 HIS A 323 -1 O LEU A 322 N LEU A 289
SHEET 1 H 3 PRO A 299 ARG A 306 0
SHEET 2 H 3 VAL A 335 ASN A 342 -1 O LYS A 339 N VAL A 303
SHEET 3 H 3 GLY A 345 VAL A 352 -1 O GLY A 345 N ASN A 342
SSBOND 1 CYS A 78 CYS A 148 1555 1555 2.79
SSBOND 2 CYS A 193 CYS A 246 1555 1555 2.05
SSBOND 3 CYS A 291 CYS A 338 1555 1555 2.05
LINK ND2 ASN A 73 C1 NAG B 1 1555 1555 1.42
LINK ND2 ASN A 125 C1 NAG C 1 1555 1555 1.43
LINK ND2 ASN A 186 C1 NAG D 1 1555 1555 1.71
LINK ND2 ASN A 222 C1 NAG E 1 1555 1555 1.45
LINK ND2 ASN A 331 C1 NAG A 420 1555 1555 1.45
LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44
LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44
LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.40
LINK O6 BMA B 3 C1 MAN B 5 1555 1555 1.40
LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40
LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.42
LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.52
LINK O6 NAG D 1 C1 FUC D 6 1555 1555 1.40
LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.43
LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.42
LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.41
LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.47
LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.46
LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.39
LINK O6 BMA E 3 C1 MAN E 5 1555 1555 1.41
CISPEP 1 GLY A 115 GLU A 116 0 4.02
CISPEP 2 PHE A 153 PRO A 154 0 3.06
CISPEP 3 LYS A 199 PRO A 200 0 -8.14
CISPEP 4 ASN A 296 PRO A 297 0 0.14
CRYST1 131.867 131.867 247.543 90.00 90.00 120.00 P 65 2 2 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 0.007583 0.004378 0.000000 0.00000
SCALE2 0.000000 0.008757 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004040 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
