HEADER HYDROLASE/PEPTIDE 20-MAY-15 4ZXL TITLE CPOGA D298N IN COMPLEX WITH DROSOPHILA HCF -DERIVED THR-O-GLCNAC TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAG-PRO-SER-THR-ALA-THR-O-GLCNAC CONTAINING PEPTIDE FROM COMPND 3 DROSOPHILA HCF; COMPND 4 CHAIN: H; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THR-O-GLCNAC CONTAINING PEPTIDE FROM DROSOPHILA HCF; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: O-GLCNACASE NAGJ; COMPND 9 CHAIN: A; COMPND 10 FRAGMENT: UNP RESIDUES 39-617; COMPND 11 SYNONYM: CPOGA,BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N- COMPND 12 ACETYLHEXOSAMINIDASE,BETA-HEXOSAMINIDASE,GH84C,HEXOSAMINIDASE B,N- COMPND 13 ACETYL-BETA-D-GLUCOSAMINIDASE; COMPND 14 EC: 3.2.1.169,3.2.1.52; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS (STRAIN ATCC 13124 / SOURCE 7 NCTC 8237 / TYPE A); SOURCE 8 ORGANISM_TAXID: 195103; SOURCE 9 GENE: NAGJ, CPF_1442; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE-O-GLCNACYLATED PEPTIDE COMPLEX TIM BARREL THR-O-GLCNAC, KEYWDS 2 HYDROLASE-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.SELVAN,D.M.F.VAN AALTEN REVDAT 3 10-JAN-24 4ZXL 1 HETSYN REVDAT 2 29-JUL-20 4ZXL 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 23-SEP-15 4ZXL 0 JRNL AUTH D.MARIAPPA,N.SELVAN,V.S.BORODKIN,J.ALONSO,A.T.FERENBACH, JRNL AUTH 2 C.SHEPHERD,I.H.NAVRATILOVA,D.M.VAN AALTEN JRNL TITL A MUTANT O-GLCNACASE AS A PROBE TO REVEAL GLOBAL DYNAMICS OF JRNL TITL 2 PROTEIN O-GLCNACYLATION DURING DROSOPHILA EMBRYONIC JRNL TITL 3 DEVELOPMENT. JRNL REF BIOCHEM.J. V. 470 255 2015 JRNL REFN ESSN 1470-8728 JRNL PMID 26348912 JRNL DOI 10.1042/BJ20150610 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 35353 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) : 0.171 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 729 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2552 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.4330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4601 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.513 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4711 ; 0.006 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6397 ; 1.007 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 581 ; 5.120 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;37.794 ;25.967 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 790 ;13.842 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;13.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 698 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3646 ; 0.003 ; 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): 4711 ; 1.467 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 35 ;45.638 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4670 ;28.239 ; 5.000 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4ZXL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000210079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8729 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36087 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 34.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.86200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 2YDS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CPOGA D298N WAS CONCENTRATED TO 35 REMARK 280 MG/ML IN 25 MM TRIS/HCL (PH 8.0) AND CRYSTALLIZED FROM 0.175 M REMARK 280 CDSO4 AND 0.6 M SODIUM ACETATE PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 49.48033 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 98.96067 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 74.22050 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 123.70083 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 24.74017 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, A 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 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 GLU A 115 CG CD OE1 OE2 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 131 -1.98 81.04 REMARK 500 SER A 166 -3.85 71.05 REMARK 500 ALA A 216 43.88 -148.61 REMARK 500 ARG A 224 -68.89 -125.67 REMARK 500 ASP A 262 19.45 -142.95 REMARK 500 PHE A 318 -59.98 -122.44 REMARK 500 PHE A 403 64.36 -163.88 REMARK 500 LYS A 488 -13.28 68.08 REMARK 500 THR A 489 -105.71 -111.63 REMARK 500 ALA A 498 69.61 21.64 REMARK 500 LYS A 515 29.09 49.33 REMARK 500 VAL A 608 -83.77 -122.88 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 CD A 702 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 51 OE2 REMARK 620 2 ASN A 450 OD1 96.2 REMARK 620 3 ASP A 452 OD1 152.0 97.7 REMARK 620 4 HOH A 838 O 81.3 177.5 84.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 701 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 58 OD2 REMARK 620 2 GLU A 272 OE2 27.9 REMARK 620 3 HOH A 857 O 117.3 96.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 704 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 68 O REMARK 620 2 GLU A 71 OE1 76.5 REMARK 620 3 GLU A 71 OE2 114.5 52.9 REMARK 620 4 HOH A 843 O 155.2 126.2 79.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 705 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 73 O REMARK 620 2 GLU A 108 OE1 112.0 REMARK 620 3 ASP A 111 OD1 93.6 113.5 REMARK 620 4 HOH A 803 O 174.0 71.0 89.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 713 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 112 OD2 REMARK 620 2 GLU A 550 OE2 31.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 706 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 117 OD1 REMARK 620 2 GLU A 145 OE2 92.0 REMARK 620 3 GLU A 545 OE1 91.5 19.6 REMARK 620 4 GLU A 545 OE2 93.9 18.8 2.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 714 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 117 OD2 REMARK 620 2 GLU A 549 OE1 68.8 REMARK 620 3 GLU A 549 OE2 69.2 0.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 707 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 139 OD1 REMARK 620 2 ASP A 139 OD2 52.8 REMARK 620 3 ASP A 268 OD2 70.1 24.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 703 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 170 OE1 REMARK 620 2 GLU A 170 OE2 56.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 709 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 272 OE1 REMARK 620 2 HIS A 276 NE2 111.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 710 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 282 OE1 REMARK 620 2 ASP A 286 OD1 87.4 REMARK 620 3 ASP A 286 OD2 79.9 53.1 REMARK 620 4 GLU A 588 OE1 53.9 41.5 35.4 REMARK 620 5 GLU A 588 OE2 54.7 41.3 34.4 1.0 REMARK 620 6 HOH A 807 O 72.8 129.4 77.5 92.4 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 711 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 362 OE1 REMARK 620 2 GLU A 362 OE2 56.6 REMARK 620 3 ASP A 424 OD1 85.8 138.2 REMARK 620 4 ASP A 424 OD2 138.5 149.7 54.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 712 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 413 NE2 REMARK 620 2 HOH A 856 O 78.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 715 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 474 OD1 REMARK 620 2 ASP A 474 OD2 51.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YDS RELATED DB: PDB REMARK 900 2YDS CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND REMARK 900 RELATED ID: 2YDR RELATED DB: PDB REMARK 900 2YDR CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND REMARK 900 RELATED ID: 2YDQ RELATED DB: PDB REMARK 900 2YDQ CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND REMARK 900 RELATED ID: 2VUR RELATED DB: PDB REMARK 900 2VUR CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND DBREF 4ZXL H 615 618 PDB 4ZXL 4ZXL 615 618 DBREF 4ZXL A 39 617 UNP Q0TR53 OGA_CLOP1 39 617 SEQADV 4ZXL ASN A 298 UNP Q0TR53 ASP 298 ENGINEERED MUTATION SEQADV 4ZXL ASP A 388 UNP Q0TR53 ASN 388 CONFLICT SEQRES 1 H 4 PRO SER THR ALA SEQRES 1 A 579 ASN GLN VAL LEU VAL PRO ASN LEU ASN PRO THR PRO GLU SEQRES 2 A 579 ASN LEU GLU VAL VAL GLY ASP GLY PHE LYS ILE THR SER SEQRES 3 A 579 SER ILE ASN LEU VAL GLY GLU GLU GLU ALA ASP GLU ASN SEQRES 4 A 579 ALA VAL ASN ALA LEU ARG GLU PHE LEU THR ALA ASN ASN SEQRES 5 A 579 ILE GLU ILE ASN SER GLU ASN ASP PRO ASN SER THR THR SEQRES 6 A 579 LEU ILE ILE GLY GLU VAL ASP ASP ASP ILE PRO GLU LEU SEQRES 7 A 579 ASP GLU ALA LEU ASN GLY THR THR ALA GLU ASN LEU LYS SEQRES 8 A 579 GLU GLU GLY TYR ALA LEU VAL SER ASN ASP GLY LYS ILE SEQRES 9 A 579 ALA ILE GLU GLY LYS ASP GLY ASP GLY THR PHE TYR GLY SEQRES 10 A 579 VAL GLN THR PHE LYS GLN LEU VAL LYS GLU SER ASN ILE SEQRES 11 A 579 PRO GLU VAL ASN ILE THR ASP TYR PRO THR VAL SER ALA SEQRES 12 A 579 ARG GLY ILE VAL GLU GLY PHE TYR GLY THR PRO TRP THR SEQRES 13 A 579 HIS GLN ASP ARG LEU ASP GLN ILE LYS PHE TYR GLY GLU SEQRES 14 A 579 ASN LYS LEU ASN THR TYR ILE TYR ALA PRO LYS ASP ASP SEQRES 15 A 579 PRO TYR HIS ARG GLU LYS TRP ARG GLU PRO TYR PRO GLU SEQRES 16 A 579 SER GLU MET GLN ARG MET GLN GLU LEU ILE ASN ALA SER SEQRES 17 A 579 ALA GLU ASN LYS VAL ASP PHE VAL PHE GLY ILE SER PRO SEQRES 18 A 579 GLY ILE ASP ILE ARG PHE ASP GLY ASP ALA GLY GLU GLU SEQRES 19 A 579 ASP PHE ASN HIS LEU ILE THR LYS ALA GLU SER LEU TYR SEQRES 20 A 579 ASP MET GLY VAL ARG SER PHE ALA ILE TYR TRP ASP ASN SEQRES 21 A 579 ILE GLN ASP LYS SER ALA ALA LYS HIS ALA GLN VAL LEU SEQRES 22 A 579 ASN ARG PHE ASN GLU GLU PHE VAL LYS ALA LYS GLY ASP SEQRES 23 A 579 VAL LYS PRO LEU ILE THR VAL PRO THR GLU TYR ASP THR SEQRES 24 A 579 GLY ALA MET VAL SER ASN GLY GLN PRO ARG ALA TYR THR SEQRES 25 A 579 ARG ILE PHE ALA GLU THR VAL ASP PRO SER ILE GLU VAL SEQRES 26 A 579 MET TRP THR GLY PRO GLY VAL VAL THR ASN GLU ILE PRO SEQRES 27 A 579 LEU SER ASP ALA GLN LEU ILE SER GLY ILE TYR ASP ARG SEQRES 28 A 579 ASN MET ALA VAL TRP TRP ASN TYR PRO VAL THR ASP TYR SEQRES 29 A 579 PHE LYS GLY LYS LEU ALA LEU GLY PRO MET HIS GLY LEU SEQRES 30 A 579 ASP LYS GLY LEU ASN GLN TYR VAL ASP PHE PHE THR VAL SEQRES 31 A 579 ASN PRO MET GLU HIS ALA GLU LEU SER LYS ILE SER ILE SEQRES 32 A 579 HIS THR ALA ALA ASP TYR SER TRP ASN MET ASP ASN TYR SEQRES 33 A 579 ASP TYR ASP LYS ALA TRP ASN ARG ALA ILE ASP MET LEU SEQRES 34 A 579 TYR GLY ASP LEU ALA GLU ASP MET LYS VAL PHE ALA ASN SEQRES 35 A 579 HIS SER THR ARG MET ASP ASN LYS THR TRP ALA LYS SER SEQRES 36 A 579 GLY ARG GLU ASP ALA PRO GLU LEU ARG ALA LYS MET ASP SEQRES 37 A 579 GLU LEU TRP ASN LYS LEU SER SER LYS GLU ASP ALA SER SEQRES 38 A 579 ALA LEU ILE GLU GLU LEU TYR GLY GLU PHE ALA ARG MET SEQRES 39 A 579 GLU GLU ALA CYS ASN ASN LEU LYS ALA ASN LEU PRO GLU SEQRES 40 A 579 VAL ALA LEU GLU GLU CYS SER ARG GLN LEU ASP GLU LEU SEQRES 41 A 579 ILE THR LEU ALA GLN GLY ASP LYS ALA SER LEU ASP MET SEQRES 42 A 579 ILE VAL ALA GLN LEU ASN GLU ASP THR GLU ALA TYR GLU SEQRES 43 A 579 SER ALA LYS GLU ILE ALA GLN ASN LYS LEU ASN THR ALA SEQRES 44 A 579 LEU SER SER PHE ALA VAL ILE SER GLU LYS VAL ALA GLN SEQRES 45 A 579 SER PHE ILE GLN GLU ALA LEU HET NAG H 701 14 HET CD A 701 1 HET CD A 702 1 HET CD A 703 1 HET CD A 704 1 HET CD A 705 1 HET CD A 706 1 HET CD A 707 1 HET CD A 708 1 HET CD A 709 1 HET CD A 710 1 HET CD A 711 1 HET CD A 712 1 HET CD A 713 1 HET CD A 714 1 HET CD A 715 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CD CADMIUM ION 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 NAG C8 H15 N O6 FORMUL 4 CD 15(CD 2+) FORMUL 19 HOH *75(H2 O) HELIX 1 AA1 ASP A 75 ASN A 89 1 15 HELIX 2 AA2 ILE A 113 LEU A 120 1 8 HELIX 3 AA3 ASP A 148 VAL A 163 1 16 HELIX 4 AA4 THR A 194 ASN A 208 1 15 HELIX 5 AA5 PRO A 232 ASN A 249 1 18 HELIX 6 AA6 ASP A 266 ASP A 286 1 21 HELIX 7 AA7 SER A 303 PHE A 318 1 16 HELIX 8 AA8 PHE A 318 GLY A 323 1 6 HELIX 9 AA9 ASP A 336 MET A 340 1 5 HELIX 10 AB1 ARG A 347 VAL A 357 1 11 HELIX 11 AB2 PRO A 376 ASP A 388 1 13 HELIX 12 AB3 GLY A 418 GLN A 421 5 4 HELIX 13 AB4 HIS A 433 ASN A 450 1 18 HELIX 14 AB5 ASP A 455 GLY A 469 1 15 HELIX 15 AB6 LEU A 471 ASN A 480 1 10 HELIX 16 AB7 ALA A 498 SER A 514 1 17 HELIX 17 AB8 ALA A 518 LEU A 543 1 26 HELIX 18 AB9 PRO A 544 ASN A 577 1 34 HELIX 19 AC1 ASP A 579 SER A 600 1 22 HELIX 20 AC2 VAL A 608 ALA A 616 1 9 SHEET 1 AA1 7 ASN A 52 VAL A 55 0 SHEET 2 AA1 7 VAL A 171 ASP A 175 -1 O ASN A 172 N GLU A 54 SHEET 3 AA1 7 TYR A 133 ASN A 138 -1 N LEU A 135 O ILE A 173 SHEET 4 AA1 7 LYS A 141 GLY A 146 -1 O ALA A 143 N VAL A 136 SHEET 5 AA1 7 THR A 102 GLU A 108 1 N ILE A 105 O ILE A 142 SHEET 6 AA1 7 SER A 65 VAL A 69 1 N ASN A 67 O LEU A 104 SHEET 7 AA1 7 GLU A 92 ILE A 93 1 O GLU A 92 N ILE A 66 SHEET 1 AA2 2 PHE A 60 LYS A 61 0 SHEET 2 AA2 2 ASN A 167 ILE A 168 -1 O ILE A 168 N PHE A 60 SHEET 1 AA3 9 ALA A 181 GLU A 186 0 SHEET 2 AA3 9 THR A 212 TYR A 215 1 O ILE A 214 N ILE A 184 SHEET 3 AA3 9 ASP A 252 ILE A 257 1 O VAL A 254 N TYR A 213 SHEET 4 AA3 9 SER A 291 TYR A 295 1 O SER A 291 N PHE A 255 SHEET 5 AA3 9 ILE A 329 VAL A 331 1 O ILE A 329 N ILE A 294 SHEET 6 AA3 9 GLU A 362 TRP A 365 1 O MET A 364 N THR A 330 SHEET 7 AA3 9 MET A 391 TRP A 395 1 O TRP A 394 N TRP A 365 SHEET 8 AA3 9 VAL A 423 VAL A 428 1 O THR A 427 N TRP A 395 SHEET 9 AA3 9 ALA A 181 GLU A 186 1 N ALA A 181 O PHE A 426 SHEET 1 AA4 2 VAL A 341 SER A 342 0 SHEET 2 AA4 2 GLN A 345 PRO A 346 -1 O GLN A 345 N SER A 342 SHEET 1 AA5 2 MET A 485 ASP A 486 0 SHEET 2 AA5 2 LYS A 492 SER A 493 -1 O SER A 493 N MET A 485 LINK OG1 THR H 617 C1 NAG H 701 1555 1555 1.47 LINK OE2 GLU A 51 CD CD A 702 1555 1555 1.99 LINK OD2 ASP A 58 CD CD A 701 1555 1555 2.01 LINK O LEU A 68 CD CD A 704 1555 1555 2.14 LINK OE1 GLU A 71 CD CD A 704 1555 1555 2.55 LINK OE2 GLU A 71 CD CD A 704 1555 1555 2.38 LINK O GLU A 73 CD CD A 705 1555 1555 2.23 LINK OE1 GLU A 108 CD CD A 705 1555 1555 2.07 LINK OD1 ASP A 111 CD CD A 705 1555 1555 2.59 LINK OD2 ASP A 112 CD CD A 713 1555 2545 2.31 LINK OD1 ASP A 117 CD CD A 706 1555 1555 2.15 LINK OD2 ASP A 117 CD CD A 714 1555 2545 2.44 LINK OD1 ASP A 139 CD CD A 707 1555 1555 2.66 LINK OD2 ASP A 139 CD CD A 707 1555 1555 2.18 LINK OE2 GLU A 145 CD CD A 706 1555 1555 2.44 LINK OE1 GLU A 170 CD CD A 703 1555 1555 2.20 LINK OE2 GLU A 170 CD CD A 703 1555 1555 2.41 LINK OD1 ASP A 252 CD CD A 708 1555 1555 2.36 LINK OD2 ASP A 268 CD CD A 707 1555 5554 2.24 LINK OE2 GLU A 272 CD CD A 701 1555 5554 2.22 LINK OE1 GLU A 272 CD CD A 709 1555 1555 2.24 LINK NE2 HIS A 276 CD CD A 709 1555 1555 2.46 LINK OE1 GLU A 282 CD CD A 710 1555 1555 2.26 LINK OD1 ASP A 286 CD CD A 710 1555 1555 2.44 LINK OD2 ASP A 286 CD CD A 710 1555 1555 2.46 LINK OE1 GLU A 362 CD CD A 711 1555 1555 2.48 LINK OE2 GLU A 362 CD CD A 711 1555 1555 2.12 LINK NE2 HIS A 413 CD CD A 712 1555 1555 2.30 LINK OD1 ASP A 424 CD CD A 711 1555 1555 2.57 LINK OD2 ASP A 424 CD CD A 711 1555 1555 2.12 LINK OD1 ASN A 450 CD CD A 702 1555 1555 2.33 LINK OD1 ASP A 452 CD CD A 702 1555 1555 2.28 LINK OD1 ASP A 474 CD CD A 715 1555 1555 2.62 LINK OD2 ASP A 474 CD CD A 715 1555 1555 2.46 LINK OE1 GLU A 545 CD CD A 706 1555 3654 2.28 LINK OE2 GLU A 545 CD CD A 706 1555 3654 2.49 LINK OE1 GLU A 549 CD CD A 714 1555 1555 2.38 LINK OE2 GLU A 549 CD CD A 714 1555 1555 2.44 LINK OE2 GLU A 550 CD CD A 713 1555 1555 1.92 LINK OE1 GLU A 588 CD CD A 710 1555 3654 2.61 LINK OE2 GLU A 588 CD CD A 710 1555 3654 2.37 LINK CD CD A 701 O HOH A 857 1555 1555 2.32 LINK CD CD A 702 O HOH A 838 1555 1555 2.39 LINK CD CD A 704 O HOH A 843 1555 1555 2.45 LINK CD CD A 705 O HOH A 803 1555 1555 2.29 LINK CD CD A 710 O HOH A 807 1555 1555 2.19 LINK CD CD A 712 O HOH A 856 1555 1555 2.57 CISPEP 1 ASN A 47 PRO A 48 0 -1.47 CISPEP 2 TYR A 397 PRO A 398 0 10.13 CRYST1 118.560 118.560 148.441 90.00 90.00 120.00 P 61 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 0.008435 0.004870 0.000000 0.00000 SCALE2 0.000000 0.009739 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006737 0.00000