HEADER SUGAR BINDING PROTEIN 26-DEC-13 3WOG TITLE CRYSTAL STRUCTURE PLANT LECTIN IN COMPLEX WITH LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERYTHROAGGLUTININ; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 22-275; COMPND 5 SYNONYM: PHYTOHEMAGGLUTININ SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHASEOLUS VULGARIS; SOURCE 3 ORGANISM_COMMON: KIDNEY BEAN; SOURCE 4 ORGANISM_TAXID: 3885 KEYWDS LEGUME LECTIN, COMPLEX-TYPE N-GLYCAN CONTAINING BISECTING GLCNAC, KEYWDS 2 SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.NAGAE,Y.YAMAGUCHI REVDAT 4 08-NOV-23 3WOG 1 HETSYN REVDAT 3 29-JUL-20 3WOG 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 22-NOV-17 3WOG 1 REMARK REVDAT 1 09-APR-14 3WOG 0 JRNL AUTH M.NAGAE,K.SOGA,K.MORITA-MATSUMOTO,S.HANASHIMA,A.IKEDA, JRNL AUTH 2 K.YAMAMOTO,Y.YAMAGUCHI JRNL TITL PHYTOHEMAGGLUTININ FROM PHASEOLUS VULGARIS (PHA-E) DISPLAYS JRNL TITL 2 A NOVEL GLYCAN RECOGNITION MODE USING A COMMON LEGUME LECTIN JRNL TITL 3 FOLD JRNL REF GLYCOBIOLOGY V. 24 368 2014 JRNL REFN ISSN 0959-6658 JRNL PMID 24436051 JRNL DOI 10.1093/GLYCOB/CWU004 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 47080 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) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2532 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3221 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 190 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3706 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.44000 REMARK 3 B22 (A**2) : 1.11000 REMARK 3 B33 (A**2) : -2.54000 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): 0.167 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.797 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3900 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5294 ; 1.316 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 6.786 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;35.546 ;25.188 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 595 ;13.975 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;13.748 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 638 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2879 ; 0.005 ; 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): 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 : NULL 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: NULL REMARK 4 REMARK 4 3WOG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000096591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 LIQUID NITROGEN COOLING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49885 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 36.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49400 REMARK 200 FOR SHELL : 6.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3WCS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS (PH 5.5), 2.0M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 48.91450 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 48.91450 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 38.39000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 97.74050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.39000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 97.74050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.91450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.39000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 97.74050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.91450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.39000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 97.74050 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -48.91450 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 THR A 260 REMARK 465 SER A 261 REMARK 465 GLU A 262 REMARK 465 ALA A 263 REMARK 465 LEU A 264 REMARK 465 ASN A 265 REMARK 465 LEU A 266 REMARK 465 ALA A 267 REMARK 465 ASN A 268 REMARK 465 PHE A 269 REMARK 465 ALA A 270 REMARK 465 LEU A 271 REMARK 465 ASN A 272 REMARK 465 GLN A 273 REMARK 465 ILE A 274 REMARK 465 LEU A 275 REMARK 465 ASP B 257 REMARK 465 GLY B 258 REMARK 465 THR B 259 REMARK 465 THR B 260 REMARK 465 SER B 261 REMARK 465 GLU B 262 REMARK 465 ALA B 263 REMARK 465 ASN B 272 REMARK 465 GLN B 273 REMARK 465 ILE B 274 REMARK 465 LEU B 275 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 ARG A 41 -116.95 57.98 REMARK 500 ALA A 106 148.88 -173.35 REMARK 500 LYS A 121 -147.39 -100.94 REMARK 500 TRP A 154 -21.96 -152.52 REMARK 500 ASN A 166 15.90 58.39 REMARK 500 LYS A 238 133.44 -37.55 REMARK 500 ARG B 41 -122.61 44.27 REMARK 500 ASN B 57 -169.85 -65.44 REMARK 500 SER B 65 14.38 59.10 REMARK 500 LYS B 121 -153.05 -105.07 REMARK 500 LYS B 123 -156.88 -79.01 REMARK 500 LEU B 127 18.18 57.36 REMARK 500 TRP B 154 -23.32 -153.94 REMARK 500 ASN B 166 17.94 58.16 REMARK 500 LYS B 195 19.52 52.86 REMARK 500 LYS B 238 130.09 -35.44 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 MN A1002 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 145 OE2 REMARK 620 2 ASP A 147 OD2 102.8 REMARK 620 3 ASP A 155 OD1 169.0 86.2 REMARK 620 4 HIS A 160 NE2 90.0 94.7 95.6 REMARK 620 5 HOH A1101 O 82.7 174.0 88.1 87.7 REMARK 620 6 HOH A1102 O 84.5 91.8 89.0 172.3 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 147 OD1 REMARK 620 2 ASP A 147 OD2 56.6 REMARK 620 3 LEU A 149 O 78.6 114.9 REMARK 620 4 ASN A 151 OD1 151.7 151.7 84.2 REMARK 620 5 ASP A 155 OD2 114.7 78.2 81.8 84.4 REMARK 620 6 HOH A1103 O 113.5 74.1 168.0 84.6 92.7 REMARK 620 7 HOH A1104 O 76.0 117.9 88.8 81.4 163.7 93.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1002 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 145 OE2 REMARK 620 2 ASP B 147 OD2 98.9 REMARK 620 3 ASP B 155 OD1 166.8 91.5 REMARK 620 4 HIS B 160 NE2 93.4 93.1 94.2 REMARK 620 5 HOH B1104 O 87.4 173.4 82.6 84.6 REMARK 620 6 HOH B1105 O 80.4 93.2 90.9 171.8 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 147 OD1 REMARK 620 2 ASP B 147 OD2 55.5 REMARK 620 3 LEU B 149 O 75.3 113.6 REMARK 620 4 ASN B 151 OD1 146.0 157.4 77.3 REMARK 620 5 ASP B 155 OD2 113.7 77.5 86.2 83.8 REMARK 620 6 HOH B1106 O 114.9 79.7 166.7 90.1 96.6 REMARK 620 7 HOH B1107 O 74.3 117.5 82.5 82.7 164.0 92.0 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WCR RELATED DB: PDB REMARK 900 RELATED ID: 3WCS RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE OF THE PROTEIN HAS BEEN DEPOSITED TO DDBJ WITH ACCESSION REMARK 999 NUMBER AB823629-1, PROTEIN ID BAO18728.1 DBREF 3WOG A 22 275 UNP V5YN37 V5YN37_PHAVU 22 275 DBREF 3WOG B 22 275 UNP V5YN37 V5YN37_PHAVU 22 275 SEQRES 1 A 254 ALA SER GLN THR SER PHE SER PHE GLN ARG PHE ASN GLU SEQRES 2 A 254 THR ASN LEU ILE LEU GLN ARG ASP ALA THR VAL SER SER SEQRES 3 A 254 LYS GLY GLN LEU ARG LEU THR ASN VAL ASN ASP ASN GLY SEQRES 4 A 254 GLU PRO THR LEU SER SER LEU GLY ARG ALA PHE TYR SER SEQRES 5 A 254 ALA PRO ILE GLN ILE TRP ASP ASN THR THR GLY ALA VAL SEQRES 6 A 254 ALA SER PHE ALA THR SER PHE THR PHE ASN ILE ASP VAL SEQRES 7 A 254 PRO ASN ASN SER GLY PRO ALA ASP GLY LEU ALA PHE VAL SEQRES 8 A 254 LEU LEU PRO VAL GLY SER GLN PRO LYS ASP LYS GLY GLY SEQRES 9 A 254 LEU LEU GLY LEU PHE ASN ASN TYR LYS TYR ASP SER ASN SEQRES 10 A 254 ALA HIS THR VAL ALA VAL GLU PHE ASP THR LEU TYR ASN SEQRES 11 A 254 VAL HIS TRP ASP PRO LYS PRO ARG HIS ILE GLY ILE ASP SEQRES 12 A 254 VAL ASN SER ILE LYS SER ILE LYS THR THR THR TRP ASP SEQRES 13 A 254 PHE VAL LYS GLY GLU ASN ALA GLU VAL LEU ILE THR TYR SEQRES 14 A 254 ASP SER SER THR LYS LEU LEU VAL ALA SER LEU VAL TYR SEQRES 15 A 254 PRO SER LEU LYS THR SER PHE ILE VAL SER ASP THR VAL SEQRES 16 A 254 ASP LEU LYS SER VAL LEU PRO GLU TRP VAL ILE VAL GLY SEQRES 17 A 254 PHE THR ALA THR THR GLY ILE THR LYS GLY ASN VAL GLU SEQRES 18 A 254 THR ASN ASP ILE LEU SER TRP SER PHE ALA SER LYS LEU SEQRES 19 A 254 SER ASP GLY THR THR SER GLU ALA LEU ASN LEU ALA ASN SEQRES 20 A 254 PHE ALA LEU ASN GLN ILE LEU SEQRES 1 B 254 ALA SER GLN THR SER PHE SER PHE GLN ARG PHE ASN GLU SEQRES 2 B 254 THR ASN LEU ILE LEU GLN ARG ASP ALA THR VAL SER SER SEQRES 3 B 254 LYS GLY GLN LEU ARG LEU THR ASN VAL ASN ASP ASN GLY SEQRES 4 B 254 GLU PRO THR LEU SER SER LEU GLY ARG ALA PHE TYR SER SEQRES 5 B 254 ALA PRO ILE GLN ILE TRP ASP ASN THR THR GLY ALA VAL SEQRES 6 B 254 ALA SER PHE ALA THR SER PHE THR PHE ASN ILE ASP VAL SEQRES 7 B 254 PRO ASN ASN SER GLY PRO ALA ASP GLY LEU ALA PHE VAL SEQRES 8 B 254 LEU LEU PRO VAL GLY SER GLN PRO LYS ASP LYS GLY GLY SEQRES 9 B 254 LEU LEU GLY LEU PHE ASN ASN TYR LYS TYR ASP SER ASN SEQRES 10 B 254 ALA HIS THR VAL ALA VAL GLU PHE ASP THR LEU TYR ASN SEQRES 11 B 254 VAL HIS TRP ASP PRO LYS PRO ARG HIS ILE GLY ILE ASP SEQRES 12 B 254 VAL ASN SER ILE LYS SER ILE LYS THR THR THR TRP ASP SEQRES 13 B 254 PHE VAL LYS GLY GLU ASN ALA GLU VAL LEU ILE THR TYR SEQRES 14 B 254 ASP SER SER THR LYS LEU LEU VAL ALA SER LEU VAL TYR SEQRES 15 B 254 PRO SER LEU LYS THR SER PHE ILE VAL SER ASP THR VAL SEQRES 16 B 254 ASP LEU LYS SER VAL LEU PRO GLU TRP VAL ILE VAL GLY SEQRES 17 B 254 PHE THR ALA THR THR GLY ILE THR LYS GLY ASN VAL GLU SEQRES 18 B 254 THR ASN ASP ILE LEU SER TRP SER PHE ALA SER LYS LEU SEQRES 19 B 254 SER ASP GLY THR THR SER GLU ALA LEU ASN LEU ALA ASN SEQRES 20 B 254 PHE ALA LEU ASN GLN ILE LEU MODRES 3WOG ASN A 33 ASN GLYCOSYLATION SITE MODRES 3WOG ASN B 33 ASN GLYCOSYLATION SITE HET MAN C 1 12 HET NAG C 2 14 HET MAN D 1 12 HET NAG D 2 14 HET NAG A1001 14 HET MN A1002 1 HET CA A1003 1 HET NAG B1001 14 HET MN B1002 1 HET CA B1003 1 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE 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 FORMUL 3 MAN 2(C6 H12 O6) FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 6 MN 2(MN 2+) FORMUL 7 CA 2(CA 2+) FORMUL 11 HOH *52(H2 O) HELIX 1 1 ASN A 33 THR A 35 5 3 HELIX 2 2 LYS A 123 LEU A 127 5 5 HELIX 3 3 ASP A 217 LEU A 222 1 6 HELIX 4 4 ASN B 33 THR B 35 5 3 HELIX 5 5 LYS B 123 LEU B 127 5 5 HELIX 6 6 ASP B 217 LEU B 222 1 6 HELIX 7 7 ASN B 265 LEU B 271 1 7 SHEET 1 A 4 SER A 23 PHE A 29 0 SHEET 2 A 4 ASP A 245 LEU A 255 -1 O TRP A 249 N PHE A 29 SHEET 3 A 4 LEU A 51 ARG A 52 -1 N LEU A 51 O ILE A 246 SHEET 4 A 4 THR A 44 VAL A 45 -1 N THR A 44 O ARG A 52 SHEET 1 B 6 SER A 23 PHE A 29 0 SHEET 2 B 6 ASP A 245 LEU A 255 -1 O TRP A 249 N PHE A 29 SHEET 3 B 6 SER A 88 ASN A 96 -1 N THR A 94 O LEU A 247 SHEET 4 B 6 ALA A 184 ASP A 191 -1 O VAL A 186 N PHE A 93 SHEET 5 B 6 LEU A 196 TYR A 203 -1 O VAL A 202 N GLU A 185 SHEET 6 B 6 THR A 208 THR A 215 -1 O ASP A 214 N LEU A 197 SHEET 1 C 4 LEU A 37 ARG A 41 0 SHEET 2 C 4 LEU A 67 TYR A 72 -1 O ARG A 69 N GLN A 40 SHEET 3 C 4 TRP A 225 THR A 234 -1 O PHE A 230 N ALA A 70 SHEET 4 C 4 ILE A 76 GLN A 77 -1 N ILE A 76 O VAL A 226 SHEET 1 D 7 LEU A 37 ARG A 41 0 SHEET 2 D 7 LEU A 67 TYR A 72 -1 O ARG A 69 N GLN A 40 SHEET 3 D 7 TRP A 225 THR A 234 -1 O PHE A 230 N ALA A 70 SHEET 4 D 7 ASP A 107 PRO A 115 -1 N LEU A 114 O ILE A 227 SHEET 5 D 7 VAL A 142 ASP A 147 -1 O PHE A 146 N LEU A 109 SHEET 6 D 7 HIS A 160 VAL A 165 -1 O ASP A 164 N ALA A 143 SHEET 7 D 7 LYS A 172 THR A 175 -1 O THR A 174 N ILE A 161 SHEET 1 E 4 SER B 23 PHE B 29 0 SHEET 2 E 4 THR B 243 LEU B 255 -1 O TRP B 249 N PHE B 29 SHEET 3 E 4 LEU B 51 ARG B 52 -1 N LEU B 51 O ILE B 246 SHEET 4 E 4 THR B 44 VAL B 45 -1 N THR B 44 O ARG B 52 SHEET 1 F 6 SER B 23 PHE B 29 0 SHEET 2 F 6 THR B 243 LEU B 255 -1 O TRP B 249 N PHE B 29 SHEET 3 F 6 SER B 88 ASP B 98 -1 N SER B 92 O SER B 250 SHEET 4 F 6 ALA B 184 ASP B 191 -1 O ILE B 188 N THR B 91 SHEET 5 F 6 LEU B 196 TYR B 203 -1 O VAL B 202 N GLU B 185 SHEET 6 F 6 THR B 208 THR B 215 -1 O VAL B 212 N ALA B 199 SHEET 1 G 4 LEU B 37 ARG B 41 0 SHEET 2 G 4 LEU B 67 TYR B 72 -1 O PHE B 71 N ILE B 38 SHEET 3 G 4 TRP B 225 THR B 234 -1 O PHE B 230 N ALA B 70 SHEET 4 G 4 ILE B 76 GLN B 77 -1 N ILE B 76 O VAL B 226 SHEET 1 H 7 LEU B 37 ARG B 41 0 SHEET 2 H 7 LEU B 67 TYR B 72 -1 O PHE B 71 N ILE B 38 SHEET 3 H 7 TRP B 225 THR B 234 -1 O PHE B 230 N ALA B 70 SHEET 4 H 7 ASP B 107 PRO B 115 -1 N ALA B 110 O THR B 231 SHEET 5 H 7 VAL B 142 ASP B 147 -1 O PHE B 146 N LEU B 109 SHEET 6 H 7 HIS B 160 VAL B 165 -1 O ASP B 164 N ALA B 143 SHEET 7 H 7 LYS B 172 THR B 175 -1 O LYS B 172 N ILE B 163 LINK ND2 ASN A 33 C1 NAG A1001 1555 1555 1.44 LINK ND2 ASN B 33 C1 NAG B1001 1555 1555 1.45 LINK O2 MAN C 1 C1 NAG C 2 1555 1555 1.44 LINK O2 MAN D 1 C1 NAG D 2 1555 1555 1.43 LINK OE2 GLU A 145 MN MN A1002 1555 1555 1.98 LINK OD2 ASP A 147 MN MN A1002 1555 1555 1.99 LINK OD1 ASP A 147 CA CA A1003 1555 1555 2.33 LINK OD2 ASP A 147 CA CA A1003 1555 1555 2.37 LINK O LEU A 149 CA CA A1003 1555 1555 2.36 LINK OD1 ASN A 151 CA CA A1003 1555 1555 2.31 LINK OD1 ASP A 155 MN MN A1002 1555 1555 2.00 LINK OD2 ASP A 155 CA CA A1003 1555 1555 2.32 LINK NE2 HIS A 160 MN MN A1002 1555 1555 1.98 LINK MN MN A1002 O HOH A1101 1555 1555 1.95 LINK MN MN A1002 O HOH A1102 1555 1555 1.94 LINK CA CA A1003 O HOH A1103 1555 1555 2.34 LINK CA CA A1003 O HOH A1104 1555 1555 2.32 LINK OE2 GLU B 145 MN MN B1002 1555 1555 1.97 LINK OD2 ASP B 147 MN MN B1002 1555 1555 1.95 LINK OD1 ASP B 147 CA CA B1003 1555 1555 2.33 LINK OD2 ASP B 147 CA CA B1003 1555 1555 2.37 LINK O LEU B 149 CA CA B1003 1555 1555 2.31 LINK OD1 ASN B 151 CA CA B1003 1555 1555 2.34 LINK OD1 ASP B 155 MN MN B1002 1555 1555 1.97 LINK OD2 ASP B 155 CA CA B1003 1555 1555 2.31 LINK NE2 HIS B 160 MN MN B1002 1555 1555 1.94 LINK MN MN B1002 O HOH B1104 1555 1555 1.93 LINK MN MN B1002 O HOH B1105 1555 1555 1.93 LINK CA CA B1003 O HOH B1106 1555 1555 2.31 LINK CA CA B1003 O HOH B1107 1555 1555 2.32 CISPEP 1 ALA A 106 ASP A 107 0 -3.11 CISPEP 2 ALA B 106 ASP B 107 0 -6.04 CRYST1 76.780 195.481 97.829 90.00 90.00 90.00 C 2 2 21 16 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 0.013024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010222 0.00000