PDB Short entry for 1Y4J HEADER SUGAR BINDING PROTEIN 01-DEC-04 1Y4J TITLE CRYSTAL STRUCTURE OF THE PARALOGUE OF THE HUMAN FORMYLGLYCINE TITLE 2 GENERATING ENZYME CAVEAT 1Y4J NAG D 1 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SULFATASE MODIFYING FACTOR 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: C-ALPHA-FORMYGLYCINE- GENERATING ENZYME 2, UNQ1968/PRO4500; COMPND 5 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: SUMF2; SOURCE 6 OTHER_DETAILS: HT1080 CELLS KEYWDS FORMYLGLYCINE, SULFATASES, MULTIPLE SULFATASE DEFICIENCY, HOMODIMER, KEYWDS 2 DUF323, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.DICKMANNS,M.G.RUDOLPH,R.FICNER REVDAT 6 29-JUL-20 1Y4J 1 CAVEAT COMPND REMARK SEQADV REVDAT 6 2 1 HETNAM LINK SITE ATOM REVDAT 5 26-NOV-14 1Y4J 1 REMARK REVDAT 4 13-JUL-11 1Y4J 1 VERSN REVDAT 3 24-FEB-09 1Y4J 1 VERSN REVDAT 2 19-APR-05 1Y4J 1 JRNL REVDAT 1 08-FEB-05 1Y4J 0 JRNL AUTH A.DICKMANNS,B.SCHMIDT,M.G.RUDOLPH,M.MARIAPPAN,T.DIERKS, JRNL AUTH 2 K.VON FIGURA,R.FICNER JRNL TITL CRYSTAL STRUCTURE OF HUMAN PFGE, THE PARALOG OF THE JRNL TITL 2 C{ALPHA}-FORMYLGLYCINE-GENERATING ENZYME JRNL REF J.BIOL.CHEM. V. 280 15180 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15687489 JRNL DOI 10.1074/JBC.M414317200 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 45026 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2387 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3065 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 155 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4283 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 562 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.29000 REMARK 3 B22 (A**2) : -0.61000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.427 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4558 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3945 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6190 ; 1.338 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9137 ; 0.811 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 531 ; 6.606 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;30.339 ;22.757 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 698 ;14.850 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 49 ;16.948 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 612 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5114 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1047 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 889 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4174 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2231 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2437 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 454 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.091 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 21 ; 0.142 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 66 ; 0.257 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.174 ; 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): 2738 ; 0.925 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1086 ; 0.185 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4257 ; 1.413 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2163 ; 1.906 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1933 ; 2.857 ; 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 : 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 : BABINET MODEL WITH 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 1Y4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47438 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS 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 (%): 45.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS/HCL, MPD, CACL2, PEG8000, PH 8.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 50.37500 REMARK 290 SMTRY3 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY COULD BE THE DIMER IN THE REMARK 300 ASYMMETRIC UNIT 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 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 ALA A 27 REMARK 465 THR A 109 REMARK 465 GLY A 295 REMARK 465 ARG A 296 REMARK 465 PRO A 297 REMARK 465 PRO A 298 REMARK 465 GLY A 299 REMARK 465 GLU A 300 REMARK 465 LEU A 301 REMARK 465 ARG A 302 REMARK 465 GLY A 303 REMARK 465 SER A 304 REMARK 465 HIS A 305 REMARK 465 HIS A 306 REMARK 465 HIS A 307 REMARK 465 HIS A 308 REMARK 465 HIS A 309 REMARK 465 HIS A 310 REMARK 465 GLY B 295 REMARK 465 ARG B 296 REMARK 465 PRO B 297 REMARK 465 PRO B 298 REMARK 465 GLY B 299 REMARK 465 GLU B 300 REMARK 465 LEU B 301 REMARK 465 ARG B 302 REMARK 465 GLY B 303 REMARK 465 SER B 304 REMARK 465 HIS B 305 REMARK 465 HIS B 306 REMARK 465 HIS B 307 REMARK 465 HIS B 308 REMARK 465 HIS B 309 REMARK 465 HIS B 310 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 106 CG OD1 ND2 REMARK 470 LYS B 107 CG CD CE NZ 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 ND2 ASN A 191 O5 NAG C 1 2.11 REMARK 500 O2 FUC C 3 O HOH A 1226 2.13 REMARK 500 OG SER B 29 O HOH B 2152 2.15 REMARK 500 OD1 ASP A 49 OH TYR A 242 2.16 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 LYS A 107 72.06 -119.62 REMARK 500 LEU A 116 -118.25 47.22 REMARK 500 LYS A 161 -163.58 -118.81 REMARK 500 LEU A 195 -166.28 -121.24 REMARK 500 ASN A 233 -87.34 72.20 REMARK 500 GLN A 243 -151.35 54.50 REMARK 500 ALA A 255 175.17 68.87 REMARK 500 ASN A 266 -132.80 56.25 REMARK 500 THR B 28 -179.29 -63.82 REMARK 500 LEU B 116 -117.50 47.53 REMARK 500 ARG B 139 43.46 -146.41 REMARK 500 LYS B 161 -161.94 -123.48 REMARK 500 LEU B 195 -163.32 -119.86 REMARK 500 ASN B 233 -85.01 69.69 REMARK 500 GLN B 243 -137.94 50.99 REMARK 500 ALA B 255 174.65 67.26 REMARK 500 ASN B 266 -134.78 58.53 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 A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 194 OD1 REMARK 620 2 LEU A 195 O 93.8 REMARK 620 3 ASP A 208 OD1 92.8 123.2 REMARK 620 4 ASP A 208 OD2 92.0 74.2 49.2 REMARK 620 5 PHE A 210 O 100.6 156.6 74.8 123.2 REMARK 620 6 HOH A1006 O 100.2 77.6 154.9 149.9 81.7 REMARK 620 7 HOH A1018 O 173.5 81.8 85.7 82.2 85.2 83.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1004 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 229 O REMARK 620 2 LEU A 230 O 79.2 REMARK 620 3 GLY A 232 O 87.5 98.9 REMARK 620 4 VAL A 234 O 152.7 128.0 86.4 REMARK 620 5 GLU A 236 OE2 76.3 98.2 153.7 98.5 REMARK 620 6 HOH A1047 O 68.3 147.5 82.1 84.5 72.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 194 OD1 REMARK 620 2 LEU B 195 O 95.6 REMARK 620 3 ASP B 208 OD1 91.2 123.9 REMARK 620 4 ASP B 208 OD2 86.6 75.2 49.7 REMARK 620 5 PHE B 210 O 94.8 155.0 78.4 128.1 REMARK 620 6 HOH B2021 O 175.9 84.0 85.7 89.4 87.2 REMARK 620 7 HOH B2025 O 97.0 77.9 155.9 153.1 78.3 86.9 REMARK 620 N 1 2 3 4 5 6 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 229 O REMARK 620 2 LEU B 230 O 81.6 REMARK 620 3 GLY B 232 O 86.7 98.1 REMARK 620 4 VAL B 234 O 151.4 126.5 84.0 REMARK 620 5 GLU B 236 OE2 76.0 96.9 155.1 102.6 REMARK 620 6 HOH B2059 O 68.5 150.0 78.6 83.2 78.4 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y1E RELATED DB: PDB REMARK 900 RELATED ID: 1Y1F RELATED DB: PDB REMARK 900 RELATED ID: 1Y1G RELATED DB: PDB REMARK 900 RELATED ID: 1Y1H RELATED DB: PDB REMARK 900 RELATED ID: 1Y1I RELATED DB: PDB REMARK 900 RELATED ID: 1Y1J RELATED DB: PDB DBREF 1Y4J A 27 301 UNP Q8NBJ7 SUM2_HUMAN 27 301 DBREF 1Y4J B 27 301 UNP Q8NBJ7 SUM2_HUMAN 27 301 SEQADV 1Y4J ARG A 302 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J GLY A 303 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J SER A 304 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS A 305 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS A 306 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS A 307 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS A 308 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS A 309 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS A 310 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J ARG B 302 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J GLY B 303 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J SER B 304 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS B 305 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS B 306 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS B 307 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS B 308 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS B 309 UNP Q8NBJ7 EXPRESSION TAG SEQADV 1Y4J HIS B 310 UNP Q8NBJ7 EXPRESSION TAG SEQRES 1 A 284 ALA THR SER MET VAL GLN LEU GLN GLY GLY ARG PHE LEU SEQRES 2 A 284 MET GLY THR ASN SER PRO ASP SER ARG ASP GLY GLU GLY SEQRES 3 A 284 PRO VAL ARG GLU ALA THR VAL LYS PRO PHE ALA ILE ASP SEQRES 4 A 284 ILE PHE PRO VAL THR ASN LYS ASP PHE ARG ASP PHE VAL SEQRES 5 A 284 ARG GLU LYS LYS TYR ARG THR GLU ALA GLU MET PHE GLY SEQRES 6 A 284 TRP SER PHE VAL PHE GLU ASP PHE VAL SER ASP GLU LEU SEQRES 7 A 284 ARG ASN LYS ALA THR GLN PRO MET LYS SER VAL LEU TRP SEQRES 8 A 284 TRP LEU PRO VAL GLU LYS ALA PHE TRP ARG GLN PRO ALA SEQRES 9 A 284 GLY PRO GLY SER GLY ILE ARG GLU ARG LEU GLU HIS PRO SEQRES 10 A 284 VAL LEU HIS VAL SER TRP ASN ASP ALA ARG ALA TYR CYS SEQRES 11 A 284 ALA TRP ARG GLY LYS ARG LEU PRO THR GLU GLU GLU TRP SEQRES 12 A 284 GLU PHE ALA ALA ARG GLY GLY LEU LYS GLY GLN VAL TYR SEQRES 13 A 284 PRO TRP GLY ASN TRP PHE GLN PRO ASN ARG THR ASN LEU SEQRES 14 A 284 TRP GLN GLY LYS PHE PRO LYS GLY ASP LYS ALA GLU ASP SEQRES 15 A 284 GLY PHE HIS GLY VAL SER PRO VAL ASN ALA PHE PRO ALA SEQRES 16 A 284 GLN ASN ASN TYR GLY LEU TYR ASP LEU LEU GLY ASN VAL SEQRES 17 A 284 TRP GLU TRP THR ALA SER PRO TYR GLN ALA ALA GLU GLN SEQRES 18 A 284 ASP MET ARG VAL LEU ARG GLY ALA SER TRP ILE ASP THR SEQRES 19 A 284 ALA ASP GLY SER ALA ASN HIS ARG ALA ARG VAL THR THR SEQRES 20 A 284 ARG MET GLY ASN THR PRO ASP SER ALA SER ASP ASN LEU SEQRES 21 A 284 GLY PHE ARG CYS ALA ALA ASP ALA GLY ARG PRO PRO GLY SEQRES 22 A 284 GLU LEU ARG GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 284 ALA THR SER MET VAL GLN LEU GLN GLY GLY ARG PHE LEU SEQRES 2 B 284 MET GLY THR ASN SER PRO ASP SER ARG ASP GLY GLU GLY SEQRES 3 B 284 PRO VAL ARG GLU ALA THR VAL LYS PRO PHE ALA ILE ASP SEQRES 4 B 284 ILE PHE PRO VAL THR ASN LYS ASP PHE ARG ASP PHE VAL SEQRES 5 B 284 ARG GLU LYS LYS TYR ARG THR GLU ALA GLU MET PHE GLY SEQRES 6 B 284 TRP SER PHE VAL PHE GLU ASP PHE VAL SER ASP GLU LEU SEQRES 7 B 284 ARG ASN LYS ALA THR GLN PRO MET LYS SER VAL LEU TRP SEQRES 8 B 284 TRP LEU PRO VAL GLU LYS ALA PHE TRP ARG GLN PRO ALA SEQRES 9 B 284 GLY PRO GLY SER GLY ILE ARG GLU ARG LEU GLU HIS PRO SEQRES 10 B 284 VAL LEU HIS VAL SER TRP ASN ASP ALA ARG ALA TYR CYS SEQRES 11 B 284 ALA TRP ARG GLY LYS ARG LEU PRO THR GLU GLU GLU TRP SEQRES 12 B 284 GLU PHE ALA ALA ARG GLY GLY LEU LYS GLY GLN VAL TYR SEQRES 13 B 284 PRO TRP GLY ASN TRP PHE GLN PRO ASN ARG THR ASN LEU SEQRES 14 B 284 TRP GLN GLY LYS PHE PRO LYS GLY ASP LYS ALA GLU ASP SEQRES 15 B 284 GLY PHE HIS GLY VAL SER PRO VAL ASN ALA PHE PRO ALA SEQRES 16 B 284 GLN ASN ASN TYR GLY LEU TYR ASP LEU LEU GLY ASN VAL SEQRES 17 B 284 TRP GLU TRP THR ALA SER PRO TYR GLN ALA ALA GLU GLN SEQRES 18 B 284 ASP MET ARG VAL LEU ARG GLY ALA SER TRP ILE ASP THR SEQRES 19 B 284 ALA ASP GLY SER ALA ASN HIS ARG ALA ARG VAL THR THR SEQRES 20 B 284 ARG MET GLY ASN THR PRO ASP SER ALA SER ASP ASN LEU SEQRES 21 B 284 GLY PHE ARG CYS ALA ALA ASP ALA GLY ARG PRO PRO GLY SEQRES 22 B 284 GLU LEU ARG GLY SER HIS HIS HIS HIS HIS HIS MODRES 1Y4J ASN A 191 ASN GLYCOSYLATION SITE MODRES 1Y4J ASN B 191 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET FUC C 3 10 HET NAG D 1 14 HET NAG D 2 14 HET CA A1001 1 HET CA A1004 1 HET CA B1002 1 HET CA B1003 1 HET MPD B2001 8 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 3 FUC C6 H12 O5 FORMUL 5 CA 4(CA 2+) FORMUL 9 MPD C6 H14 O2 FORMUL 10 HOH *562(H2 O) HELIX 1 1 THR A 70 LYS A 82 1 13 HELIX 2 2 THR A 85 GLY A 91 1 7 HELIX 3 3 ASP A 98 VAL A 100 5 3 HELIX 4 4 SER A 101 LYS A 107 1 7 HELIX 5 5 SER A 148 ARG A 159 1 12 HELIX 6 6 THR A 165 GLY A 175 1 11 HELIX 7 7 ALA A 244 ASP A 248 5 5 HELIX 8 8 THR B 70 LYS B 82 1 13 HELIX 9 9 THR B 85 GLY B 91 1 7 HELIX 10 10 ASP B 98 VAL B 100 5 3 HELIX 11 11 SER B 101 ALA B 108 1 8 HELIX 12 12 ILE B 136 LEU B 140 5 5 HELIX 13 13 SER B 148 ARG B 159 1 12 HELIX 14 14 THR B 165 GLY B 175 1 11 HELIX 15 15 ALA B 244 ASP B 248 5 5 SHEET 1 A 3 MET A 30 LEU A 33 0 SHEET 2 A 3 PHE A 62 ASP A 65 -1 O PHE A 62 N LEU A 33 SHEET 3 A 3 ALA A 291 ASP A 293 -1 O ALA A 292 N ALA A 63 SHEET 1 B 2 GLY A 36 MET A 40 0 SHEET 2 B 2 ARG A 55 VAL A 59 -1 O VAL A 59 N GLY A 36 SHEET 1 C 2 TRP A 92 PHE A 96 0 SHEET 2 C 2 TRP A 118 GLU A 122 -1 O VAL A 121 N SER A 93 SHEET 1 D 4 ARG A 274 ASN A 277 0 SHEET 2 D 4 ARG A 250 ARG A 253 -1 N LEU A 252 O MET A 275 SHEET 3 D 4 TRP A 235 PRO A 241 -1 N GLU A 236 O ARG A 253 SHEET 4 D 4 LEU A 286 GLY A 287 1 O GLY A 287 N TRP A 235 SHEET 1 E 3 MET B 30 LEU B 33 0 SHEET 2 E 3 PHE B 62 ASP B 65 -1 O PHE B 62 N LEU B 33 SHEET 3 E 3 ALA B 291 ASP B 293 -1 O ALA B 292 N ALA B 63 SHEET 1 F 2 GLY B 36 MET B 40 0 SHEET 2 F 2 ARG B 55 VAL B 59 -1 O ARG B 55 N MET B 40 SHEET 1 G 2 TRP B 92 PHE B 96 0 SHEET 2 G 2 TRP B 118 GLU B 122 -1 O LEU B 119 N VAL B 95 SHEET 1 H 4 ARG B 274 ASN B 277 0 SHEET 2 H 4 ARG B 250 ARG B 253 -1 N LEU B 252 O MET B 275 SHEET 3 H 4 TRP B 235 PRO B 241 -1 N GLU B 236 O ARG B 253 SHEET 4 H 4 LEU B 286 GLY B 287 1 O GLY B 287 N TRP B 235 SSBOND 1 CYS A 156 CYS A 290 1555 1555 2.06 SSBOND 2 CYS B 156 CYS B 290 1555 1555 2.09 LINK ND2 ASN A 191 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN B 191 C1 NAG D 1 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O6 NAG C 1 C1 FUC C 3 1555 1555 1.41 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK OD1 ASN A 194 CA CA A1001 1555 1555 2.31 LINK O LEU A 195 CA CA A1001 1555 1555 2.32 LINK OD1 ASP A 208 CA CA A1001 1555 1555 2.65 LINK OD2 ASP A 208 CA CA A1001 1555 1555 2.50 LINK O PHE A 210 CA CA A1001 1555 1555 2.29 LINK O ASP A 229 CA CA A1004 1555 1555 2.59 LINK O LEU A 230 CA CA A1004 1555 1555 2.59 LINK O GLY A 232 CA CA A1004 1555 1555 2.61 LINK O VAL A 234 CA CA A1004 1555 1555 2.65 LINK OE2 GLU A 236 CA CA A1004 1555 1555 2.77 LINK CA CA A1001 O HOH A1006 1555 1555 2.36 LINK CA CA A1001 O HOH A1018 1555 1555 2.42 LINK CA CA A1004 O HOH A1047 1555 1555 2.53 LINK OD1 ASN B 194 CA CA B1002 1555 1555 2.39 LINK O LEU B 195 CA CA B1002 1555 1555 2.32 LINK OD1 ASP B 208 CA CA B1002 1555 1555 2.53 LINK OD2 ASP B 208 CA CA B1002 1555 1555 2.64 LINK O PHE B 210 CA CA B1002 1555 1555 2.29 LINK O ASP B 229 CA CA B1003 1555 1555 2.59 LINK O LEU B 230 CA CA B1003 1555 1555 2.53 LINK O GLY B 232 CA CA B1003 1555 1555 2.68 LINK O VAL B 234 CA CA B1003 1555 1555 2.56 LINK OE2 GLU B 236 CA CA B1003 1555 1555 2.77 LINK CA CA B1002 O HOH B2021 1555 1555 2.44 LINK CA CA B1002 O HOH B2025 1555 1555 2.36 LINK CA CA B1003 O HOH B2059 1555 1555 2.67 CISPEP 1 GLY A 52 PRO A 53 0 -2.70 CISPEP 2 PHE A 200 PRO A 201 0 5.20 CISPEP 3 GLY B 52 PRO B 53 0 -3.89 CISPEP 4 PHE B 200 PRO B 201 0 0.32 CRYST1 47.078 100.750 62.704 90.00 101.68 90.00 P 1 21 1 4 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 0.021241 0.000000 0.004389 0.00000 SCALE2 0.000000 0.009926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016285 0.00000