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 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 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 MASTER 387 0 10 15 22 0 0 6 0 0 0 44 END