HEADER CARBOHYDRATE BINDING PROTEIN 26-SEP-12 3VYK TITLE CRYSTAL STRUCTURE OF C-TYPE LECTIN DOMAIN OF MURINE DENDRITIC CELL TITLE 2 INHIBITORY RECEPTOR 2 IN COMPLEX WITH N-GLYCAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TYPE LECTIN DOMAIN FAMILY 4, MEMBER A4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 107-233; COMPND 5 SYNONYM: DENDRITIC CELL IMMUNORECEPTOR-2, DENDRITIC CELL INHIBITORY COMPND 6 RECEPTOR 2, MCG1050915, PROTEIN CLEC4A4; COMPND 7 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: DCIR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD VECTOR KEYWDS C-TYPE LECTIN FOLD, CELL SURFACE, CARBOHYDRATE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.NAGAE,K.YAMANAKA,S.HANASHIMA,A.IKEDA,T.SATOH,N.MATSUMOTO, AUTHOR 2 K.YAMAMOTO,Y.YAMAGUCHI REVDAT 5 20-NOV-24 3VYK 1 HETSYN REVDAT 4 29-JUL-20 3VYK 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 11-DEC-13 3VYK 1 JRNL REVDAT 2 16-OCT-13 3VYK 1 JRNL REVDAT 1 02-OCT-13 3VYK 0 JRNL AUTH M.NAGAE,K.YAMANAKA,S.HANASHIMA,A.IKEDA,K.MORITA-MATSUMOTO, JRNL AUTH 2 T.SATOH,N.MATSUMOTO,K.YAMAMOTO,Y.YAMAGUCHI JRNL TITL RECOGNITION OF BISECTING N-ACETYLGLUCOSAMINE: STRUCTURAL JRNL TITL 2 BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN JRNL TITL 3 DENDRITIC CELL INHIBITORY RECEPTOR 2 JRNL REF J.BIOL.CHEM. V. 288 33598 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 24108122 JRNL DOI 10.1074/JBC.M113.513572 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 26110 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1382 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1790 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1049 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 0.26000 REMARK 3 B12 (A**2) : -0.09000 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): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.072 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1205 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1639 ; 1.274 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 129 ; 6.165 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;34.971 ;24.828 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 176 ;11.053 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ; 5.959 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 179 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 885 ; 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 3VYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000095661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(1,1,1) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27520 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49600 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 0.2M AMMONIUM SULFATE, REMARK 280 25%(W/V) PEG3350, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 33.70400 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 16.85200 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 0.00000 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 16.85200 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 33.70400 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 105 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 GLN A 174 O HOH A 1135 2454 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 VAL A 115 -108.26 55.38 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 CA A1007 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 196 OE1 REMARK 620 2 ASN A 198 OD1 75.3 REMARK 620 3 GLU A 202 OE1 148.4 75.5 REMARK 620 4 ASN A 217 OD1 66.7 141.5 142.9 REMARK 620 5 ASP A 218 OD1 72.7 82.3 91.8 91.8 REMARK 620 6 ASP A 218 O 128.5 139.4 71.0 74.1 76.6 REMARK 620 7 MAN B 2 O3 129.8 119.6 76.1 82.6 150.0 73.5 REMARK 620 8 MAN B 2 O4 74.9 76.9 109.5 87.4 145.0 135.9 64.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VYJ RELATED DB: PDB DBREF 3VYK A 107 233 UNP Q5YIR8 Q5YIR8_MOUSE 107 233 SEQADV 3VYK GLY A 105 UNP Q5YIR8 EXPRESSION TAG SEQADV 3VYK SER A 106 UNP Q5YIR8 EXPRESSION TAG SEQRES 1 A 129 GLY SER CYS PRO LYS ASP TRP LYS PRO PHE VAL SER HIS SEQRES 2 A 129 CYS TYR PHE ILE LEU ASN ASP SER LYS ALA SER TRP ASN SEQRES 3 A 129 GLU SER GLU GLU LYS CYS SER HIS MET GLY ALA HIS LEU SEQRES 4 A 129 VAL VAL ILE HIS SER GLN ALA GLU GLN ASP PHE ILE THR SEQRES 5 A 129 SER ASN LEU ASN THR SER ALA GLY TYR PHE ILE GLY LEU SEQRES 6 A 129 LEU ASP ALA GLY GLN ARG GLN TRP ARG TRP ILE ASP GLN SEQRES 7 A 129 THR PRO TYR ASN LYS SER ALA THR PHE TRP HIS LYS GLY SEQRES 8 A 129 GLU PRO ASN GLN ASP TRP GLU ARG CYS VAL ILE ILE ASN SEQRES 9 A 129 HIS LYS THR THR GLY TRP GLY TRP ASN ASP ILE PRO CYS SEQRES 10 A 129 LYS ASP GLU HIS ASN SER VAL CYS GLN VAL LYS LYS HET MMA B 1 13 HET MAN B 2 11 HET NAG B 3 14 HET MAN B 4 11 HET NAG B 5 14 HET NAG B 6 14 HET CA A1007 1 HET SO4 A1008 5 HET SO4 A1009 5 HET EDO A1010 4 HETNAM MMA METHYL ALPHA-D-MANNOPYRANOSIDE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN MMA O1-METHYL-MANNOSE; METHYL ALPHA-D-MANNOSIDE; METHYL D- HETSYN 2 MMA MANNOSIDE; METHYL MANNOSIDE 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 HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MMA C7 H14 O6 FORMUL 2 MAN 2(C6 H12 O6) FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 CA CA 2+ FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *88(H2 O) HELIX 1 1 SER A 128 MET A 139 1 12 HELIX 2 2 SER A 148 ASN A 158 1 11 SHEET 1 A 5 LYS A 112 PHE A 114 0 SHEET 2 A 5 HIS A 117 ALA A 127 -1 O TYR A 119 N LYS A 112 SHEET 3 A 5 HIS A 225 LYS A 232 -1 O VAL A 231 N CYS A 118 SHEET 4 A 5 TYR A 165 ASP A 171 1 N PHE A 166 O ASN A 226 SHEET 5 A 5 TRP A 177 TRP A 179 -1 O ARG A 178 N LEU A 170 SHEET 1 B 5 HIS A 142 LEU A 143 0 SHEET 2 B 5 HIS A 225 LYS A 232 -1 O GLN A 230 N HIS A 142 SHEET 3 B 5 TYR A 165 ASP A 171 1 N PHE A 166 O ASN A 226 SHEET 4 B 5 CYS A 204 LYS A 210 -1 O ILE A 207 N TYR A 165 SHEET 5 B 5 GLY A 213 ILE A 219 -1 O ASN A 217 N ILE A 206 SSBOND 1 CYS A 107 CYS A 118 1555 1555 2.04 SSBOND 2 CYS A 136 CYS A 229 1555 1555 2.06 SSBOND 3 CYS A 204 CYS A 221 1555 1555 2.03 LINK O3 MMA B 1 C1 MAN B 2 1555 1555 1.44 LINK O6 MMA B 1 C1 MAN B 4 1555 1555 1.44 LINK O4 MMA B 1 C1 NAG B 6 1555 1555 1.43 LINK O2 MAN B 2 C1 NAG B 3 1555 1555 1.43 LINK O2 MAN B 4 C1 NAG B 5 1555 1555 1.44 LINK OE1 GLU A 196 CA CA A1007 1555 1555 2.40 LINK OD1 ASN A 198 CA CA A1007 1555 1555 2.37 LINK OE1 GLU A 202 CA CA A1007 1555 1555 2.36 LINK OD1 ASN A 217 CA CA A1007 1555 1555 2.36 LINK OD1 ASP A 218 CA CA A1007 1555 1555 2.33 LINK O ASP A 218 CA CA A1007 1555 1555 2.40 LINK CA CA A1007 O3 MAN B 2 1555 1555 2.38 LINK CA CA A1007 O4 MAN B 2 1555 1555 2.40 CISPEP 1 GLU A 196 PRO A 197 0 -4.04 CRYST1 76.341 76.341 50.556 90.00 90.00 120.00 P 32 2 1 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 0.013099 0.007563 0.000000 0.00000 SCALE2 0.000000 0.015126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019780 0.00000