HEADER HYDROLASE 11-NOV-14 4D6G TITLE CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE TITLE 2 (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE (L19 TITLE 3 MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSIDE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 423-1005; COMPND 5 EC: 3.2.1.102; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 406556; SOURCE 4 STRAIN: SP3-BS71; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET29 KEYWDS HYDROLASE, BLOOD GROUP ANTIGEN EXPDTA X-RAY DIFFRACTION AUTHOR D.H.KWAN,I.CONSTANTINESCU,R.CHAPANIAN,M.A.HIGGINS,E.SAMAIN, AUTHOR 2 A.B.BORASTON,J.N.KIZHAKKEDATHU,S.G.WITHERS REVDAT 6 20-DEC-23 4D6G 1 HETSYN REVDAT 5 29-JUL-20 4D6G 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 18-APR-18 4D6G 1 REMARK REVDAT 3 20-MAY-15 4D6G 1 JRNL REVDAT 2 29-APR-15 4D6G 1 JRNL REVDAT 1 26-NOV-14 4D6G 0 JRNL AUTH D.H.KWAN,I.CONSTANTINESCU,R.CHAPANIAN,M.A.HIGGINS, JRNL AUTH 2 M.KOETZLER,E.SAMAIN,A.B.BORASTON,J.N.KIZHAKKEDATHU, JRNL AUTH 3 S.G.WITHERS JRNL TITL TOWARDS EFFICIENT ENZYMES FOR THE GENERATION OF UNIVERSAL JRNL TITL 2 BLOOD THROUGH STRUCTURE-GUIDED DIRECTED EVOLUTION. JRNL REF J.AM.CHEM.SOC. V. 137 5695 2015 JRNL REFN ISSN 0002-7863 JRNL PMID 25870881 JRNL DOI 10.1021/JA5116088 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 182768 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) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.133 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9686 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) : 1.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.27 REMARK 3 REFLECTION IN BIN (WORKING SET) : 12932 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE SET COUNT : 693 REMARK 3 BIN FREE R VALUE : 0.1910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4777 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 1042 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 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): 0.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.017 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.849 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.977 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5287 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3570 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7213 ; 1.446 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8719 ; 0.929 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 652 ; 6.065 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;36.028 ;25.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 909 ;11.004 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.842 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 751 ; 0.164 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6007 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1076 ; 0.001 ; 0.020 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): 3124 ; 1.195 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1257 ; 0.390 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5088 ; 1.896 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2163 ; 2.839 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2125 ; 4.188 ; 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): 8857 ; 1.070 ; 3.000 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 : 1.40 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 4D6G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1290062280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98005 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 192579 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 48.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2WMI REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.2M AMMONIUM SULFATE, REMARK 280 0.1M SODIUM ACETATE PH 4.8 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 48.33000 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 48.33000 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 46.12500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 77.01000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.12500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 77.01000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.33000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.12500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 77.01000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.33000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.12500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 77.01000 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 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 ARG A 1008 REMARK 465 ALA A 1009 REMARK 465 PRO A 1010 REMARK 465 PRO A 1011 REMARK 465 PRO A 1012 REMARK 465 PRO A 1013 REMARK 465 PRO A 1014 REMARK 465 LEU A 1015 REMARK 465 ARG A 1016 REMARK 465 SER A 1017 REMARK 465 GLY A 1018 REMARK 465 CYS A 1019 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 421 CG CD OE1 OE2 REMARK 470 LYS A 508 CG CD CE NZ REMARK 470 GLU A 804 CG CD OE1 OE2 REMARK 470 LYS A 983 CG CD CE NZ REMARK 470 THR A1007 OG1 CG2 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 O HOH A 3461 O HOH A 4039 1.51 REMARK 500 O HOH A 3187 O HOH A 3188 1.52 REMARK 500 O HOH A 3599 O HOH A 3614 1.54 REMARK 500 O HOH A 3188 O HOH A 3333 1.55 REMARK 500 NZ LYS A 666 O HOH A 3470 1.68 REMARK 500 O HOH A 3424 O HOH A 3425 1.69 REMARK 500 O HOH A 3470 O HOH A 3471 1.71 REMARK 500 O HOH A 3492 O HOH A 3692 1.73 REMARK 500 NZ LYS A 745 O HOH A 3437 1.73 REMARK 500 O HOH A 3060 O HOH A 3062 1.76 REMARK 500 O HOH A 3439 O HOH A 3440 1.78 REMARK 500 O HOH A 3439 O HOH A 3524 1.80 REMARK 500 ND2 ASN A 762 O HOH A 3348 1.82 REMARK 500 O HOH A 3424 O HOH A 3520 1.83 REMARK 500 O HOH A 3152 O HOH A 3308 1.85 REMARK 500 O HOH A 3425 O HOH A 3524 1.86 REMARK 500 O HOH A 3131 O HOH A 3136 1.87 REMARK 500 O HOH A 3150 O HOH A 3308 1.91 REMARK 500 O HOH A 3129 O HOH A 3131 1.92 REMARK 500 NH1 ARG A 486 O HOH A 3130 1.96 REMARK 500 O HOH A 3523 O HOH A 3524 1.97 REMARK 500 O HOH A 3685 O HOH A 3691 1.97 REMARK 500 OD1 ASP A 613 O HOH A 3378 2.04 REMARK 500 O HOH A 3356 O HOH A 3463 2.05 REMARK 500 O HOH A 3456 O HOH A 3985 2.05 REMARK 500 O HOH A 3456 O HOH A 3987 2.06 REMARK 500 NZ LYS A 462 O HOH A 3083 2.09 REMARK 500 O HOH A 3877 O HOH A 3878 2.11 REMARK 500 O HOH A 3618 O HOH A 4032 2.12 REMARK 500 O HOH A 3716 O HOH A 3717 2.12 REMARK 500 O1 GLA B 1 O HOH A 3396 2.12 REMARK 500 O HOH A 3424 O HOH A 3524 2.13 REMARK 500 O HOH A 3456 O HOH A 3618 2.14 REMARK 500 NZ LYS A 753 O HOH A 3679 2.15 REMARK 500 O HOH A 3492 O HOH A 3776 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 3182 O HOH A 3498 8555 1.67 REMARK 500 O HOH A 3185 O HOH A 3490 8555 1.86 REMARK 500 O HOH A 3134 O HOH A 3711 8555 2.08 REMARK 500 O HOH A 3654 O HOH A 3654 3555 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 ASP A 481 -117.13 36.84 REMARK 500 TRP A 535 48.17 -93.43 REMARK 500 GLU A 558 78.33 64.98 REMARK 500 TRP A 667 -127.69 -132.69 REMARK 500 TRP A 667 -127.69 -132.78 REMARK 500 PHE A 670 -2.71 72.85 REMARK 500 GLN A 679 52.89 -140.23 REMARK 500 ASN A 765 -132.83 52.56 REMARK 500 VAL A 772 -67.75 -108.01 REMARK 500 ASN A 788 -131.61 36.25 REMARK 500 ASN A 788 -141.63 53.50 REMARK 500 ASP A 849 -119.81 46.72 REMARK 500 ASP A 849 -119.81 46.30 REMARK 500 ASN A 860 34.26 -142.46 REMARK 500 ASN A 872 -116.59 54.73 REMARK 500 THR A 926 162.48 75.80 REMARK 500 TYR A 938 -50.97 -122.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A3255 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A3367 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A3384 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A3458 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A3534 DISTANCE = 7.40 ANGSTROMS REMARK 525 HOH A3593 DISTANCE = 6.81 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 BETA-D-GALACTOSE (GAL): PART OF THE A-TRISACCHARIDE REMARK 600 PRODUCT. REMARK 600 ALPHA-L-FUCOSE (FUC): PART OF THE A-TRISACCHARIDE PRODUCT. REMARK 600 N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2G): PART OF THE REMARK 600 A-TRISACCHARIDE PRODUCT. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D6C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC REMARK 900 MODULE (SP3GH98) REMARK 900 RELATED ID: 4D6D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE REMARK 900 RELATED ID: 4D6E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE REMARK 900 RELATED ID: 4D6F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TETRASACCHARIDE REMARK 900 (E558A, X01 MUTANT) REMARK 900 RELATED ID: 4D6H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 1 BLOOD GROUP A- REMARK 900 TETRASACCHARIDE (E558A X02 MUTANT) REMARK 900 RELATED ID: 4D6I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 1 BLOOD GROUP A- REMARK 900 TETRASACCHARIDE (E558A L19 MUTANT) REMARK 900 RELATED ID: 4D6J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 2 BLOOD GROUP A- REMARK 900 TETRASACCHARIDE (E558A X01 MUTANT) DBREF 4D6G A 421 1003 UNP A5LBQ0 A5LBQ0_STREE 423 1005 SEQADV 4D6G HIS A 530 UNP A5LBQ0 TYR 532 ENGINEERED MUTATION SEQADV 4D6G SER A 559 UNP A5LBQ0 ASN 561 ENGINEERED MUTATION SEQADV 4D6G SER A 592 UNP A5LBQ0 ASN 594 ENGINEERED MUTATION SEQADV 4D6G LEU A 1004 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G GLU A 1005 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G HIS A 1006 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G THR A 1007 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G ARG A 1008 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G ALA A 1009 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G PRO A 1010 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G PRO A 1011 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G PRO A 1012 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G PRO A 1013 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G PRO A 1014 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G LEU A 1015 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G ARG A 1016 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G SER A 1017 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G GLY A 1018 UNP A5LBQ0 EXPRESSION TAG SEQADV 4D6G CYS A 1019 UNP A5LBQ0 EXPRESSION TAG SEQRES 1 A 599 GLU VAL ASP LYS ARG ARG GLU ILE ASN ASN GLU HIS PRO SEQRES 2 A 599 LEU LEU MET MET PRO LEU TYR ALA ASN GLY GLU GLU PHE SEQRES 3 A 599 ASN GLN GLY LYS TYR THR PHE TRP GLY GLY ASP THR LEU SEQRES 4 A 599 THR GLY LYS TRP GLU ASN ILE PRO ASP ASP LEU LYS PRO SEQRES 5 A 599 TYR THR VAL ILE GLN LEU HIS PRO ASP ASP LEU PRO LYS SEQRES 6 A 599 ARG ASP GLY ALA ALA ARG ASP PHE TYR GLU HIS MET LEU SEQRES 7 A 599 GLU GLU ALA ALA LYS TYR VAL ASN PRO LYS THR GLY LYS SEQRES 8 A 599 ASN GLU PRO ILE PRO VAL ILE LEU THR VAL TYR THR ALA SEQRES 9 A 599 GLY ASN MET PRO TYR HIS THR SER ALA HIS TRP LEU SER SEQRES 10 A 599 THR SER TRP ILE ASP LYS MET TYR GLN LYS TYR PRO ASN SEQRES 11 A 599 LEU HIS GLY ILE PHE SER THR GLU SER TYR TRP ILE TRP SEQRES 12 A 599 ALA ASN ASP ILE GLU ASN LYS ALA ALA ASP TYR LEU LYS SEQRES 13 A 599 VAL SER ALA LYS ASN GLY GLY TYR PHE ILE TRP ALA GLU SEQRES 14 A 599 GLN ASN SER GLY SER ALA ILE GLU LYS ALA PHE GLY LYS SEQRES 15 A 599 ASN GLY LYS ILE ALA PHE GLN LYS SER VAL ASP LYS TYR SEQRES 16 A 599 TRP LYS ASN LEU ILE PHE MET PHE LYS ASN THR PRO ALA SEQRES 17 A 599 ALA GLU GLY ASN ASP SER THR THR GLU SER TYR MET LYS SEQRES 18 A 599 GLY LEU TRP LEU SER ASN HIS THR TYR GLN TRP GLY GLY SEQRES 19 A 599 LEU MET ASP THR TRP LYS TRP TYR GLU THR GLY LYS TRP SEQRES 20 A 599 LYS LEU PHE ALA SER GLY ASN ILE GLY LYS SER GLN GLY SEQRES 21 A 599 ASP ARG GLN TRP LEU THR GLU PRO GLU SER MET LEU GLY SEQRES 22 A 599 GLU GLU ALA LEU GLY VAL TYR LEU ASN GLY GLY VAL VAL SEQRES 23 A 599 TYR ASN PHE GLU HIS PRO ALA TYR THR TYR GLY VAL ASN SEQRES 24 A 599 ASN LYS GLU SER LEU LEU PHE SER GLU VAL ILE LYS GLU SEQRES 25 A 599 PHE PHE ARG TYR VAL ILE ALA HIS PRO ALA PRO SER LYS SEQRES 26 A 599 GLU LYS VAL LEU GLU ASP THR LYS VAL PHE ILE HIS GLY SEQRES 27 A 599 ASP TYR SER ASN LYS GLY ASN GLY LYS PHE PHE VAL ASN SEQRES 28 A 599 VAL ASN THR ASP ARG GLU GLN THR PRO LEU TYR MET THR SEQRES 29 A 599 GLY ARG TYR ASN VAL ILE PRO ALA ILE PRO GLY VAL LEU SEQRES 30 A 599 LYS THR ASP LYS LEU LYS GLU SER VAL SER SER SER ARG SEQRES 31 A 599 ILE GLN ILE LYS GLU ILE THR SER PRO GLU PHE SER SER SEQRES 32 A 599 THR GLN ALA ARG LYS GLU TYR LEU ASN LYS LEU TYR PRO SEQRES 33 A 599 MET ASN TYR GLU GLY ASP ILE PHE ALA GLN LYS LEU ASP SEQRES 34 A 599 ASN ARG TRP PHE VAL TYR ASN TYR LYS VAL ASN GLU ASN SEQRES 35 A 599 VAL LYS GLN THR GLY LYS LEU LYS PHE ASN SER LEU GLU SEQRES 36 A 599 MET ASN VAL GLU PHE GLU PRO HIS THR TYR GLY ILE PHE SEQRES 37 A 599 GLU ARG ILE SER ASN GLY LEU LYS VAL ASN LEU ASN ASN SEQRES 38 A 599 PHE ARG THR ASN LYS ASP SER LEU TRP SER ASN ALA GLN SEQRES 39 A 599 ASP ALA ASN GLN ALA LYS LYS LEU PRO GLN LEU THR LYS SEQRES 40 A 599 LYS GLY ALA ILE LYS TRP ILE GLU GLU HIS TYR ILE LYS SEQRES 41 A 599 ASP THR GLN PHE GLY GLU LYS ARG VAL THR LYS ILE VAL SEQRES 42 A 599 LEU ARG GLY ILE ASP LYS LEU PRO THR ILE HIS SER LEU SEQRES 43 A 599 SER GLY THR ASN ASN SER TYR ASP GLN PRO SER LEU ASN SEQRES 44 A 599 PHE ASP GLN LYS ASN HIS MET VAL THR ILE THR ILE ASN SEQRES 45 A 599 SER ASN GLY ASN LEU GLU PHE GLU LEU HIS PHE LEU GLU SEQRES 46 A 599 HIS THR ARG ALA PRO PRO PRO PRO PRO LEU ARG SER GLY SEQRES 47 A 599 CYS HET GLA B 1 12 HET GAL B 1 12 HET FUC B 2 10 HET A2G B 3 28 HET EDO A2011 4 HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GLA C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 FUC C6 H12 O5 FORMUL 2 A2G C8 H15 N O6 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *1042(H2 O) HELIX 1 1 ASN A 442 ASN A 447 1 6 HELIX 2 2 THR A 458 ILE A 466 1 9 HELIX 3 3 LEU A 470 PRO A 472 5 3 HELIX 4 4 GLY A 488 TYR A 504 1 17 HELIX 5 5 GLY A 525 MET A 527 5 3 HELIX 6 6 THR A 531 LEU A 536 5 6 HELIX 7 7 SER A 537 TYR A 548 1 12 HELIX 8 8 ASP A 566 ASN A 581 1 16 HELIX 9 9 ASN A 591 GLY A 593 5 3 HELIX 10 10 SER A 594 PHE A 600 1 7 HELIX 11 11 ILE A 606 TRP A 616 1 11 HELIX 12 12 PRO A 627 GLY A 631 5 5 HELIX 13 13 ASN A 632 SER A 646 1 15 HELIX 14 14 TRP A 659 THR A 664 1 6 HELIX 15 15 GLN A 679 TRP A 684 1 6 HELIX 16 16 PRO A 688 LEU A 701 1 14 HELIX 17 17 HIS A 711 TYR A 716 1 6 HELIX 18 18 SER A 723 VAL A 729 1 7 HELIX 19 19 VAL A 729 HIS A 740 1 12 HELIX 20 20 SER A 744 THR A 752 1 9 HELIX 21 21 ASP A 759 LYS A 763 5 5 HELIX 22 22 GLY A 764 VAL A 770 5 7 HELIX 23 23 THR A 799 SER A 805 1 7 HELIX 24 24 SER A 818 SER A 822 5 5 HELIX 25 25 SER A 823 TYR A 835 1 13 HELIX 26 26 LYS A 906 SER A 911 5 6 HELIX 27 27 ASP A 915 LYS A 921 1 7 HELIX 28 28 THR A 926 TYR A 938 1 13 SHEET 1 AA 9 LEU A 434 TYR A 440 0 SHEET 2 AA 9 VAL A 706 GLU A 710 1 O TYR A 707 N MET A 436 SHEET 3 AA 9 GLN A 651 ASP A 657 1 O GLY A 654 N ASN A 708 SHEET 4 AA 9 LEU A 619 LYS A 624 1 O PHE A 621 N GLY A 653 SHEET 5 AA 9 TYR A 584 ALA A 588 1 O PHE A 585 N ILE A 620 SHEET 6 AA 9 LEU A 551 THR A 557 1 O HIS A 552 N TYR A 584 SHEET 7 AA 9 VAL A 517 THR A 523 1 O VAL A 517 N HIS A 552 SHEET 8 AA 9 THR A 474 HIS A 479 1 O ILE A 476 N ILE A 518 SHEET 9 AA 9 LEU A 434 TYR A 440 1 O LEU A 435 N VAL A 475 SHEET 1 AB 2 GLY A 717 VAL A 718 0 SHEET 2 AB 2 LYS A 721 GLU A 722 -1 O LYS A 721 N VAL A 718 SHEET 1 AC 3 ALA A 792 ILE A 793 0 SHEET 2 AC 3 VAL A 754 HIS A 757 1 O ILE A 756 N ILE A 793 SHEET 3 AC 3 GLN A 812 GLU A 815 1 O GLN A 812 N PHE A 755 SHEET 1 AD 6 PHE A 844 LEU A 848 0 SHEET 2 AD 6 ARG A 851 TYR A 855 -1 O ARG A 851 N LEU A 848 SHEET 3 AD 6 TYR A 885 ILE A 891 -1 O GLY A 886 N VAL A 854 SHEET 4 AD 6 GLY A 894 ASN A 900 -1 O GLY A 894 N ILE A 891 SHEET 5 AD 6 ASN A 996 HIS A1002 -1 O LEU A 997 N LEU A 899 SHEET 6 AD 6 THR A 962 GLY A 968 -1 O THR A 962 N HIS A1002 SHEET 1 AE 5 GLN A 865 PHE A 871 0 SHEET 2 AE 5 LEU A 874 PHE A 880 -1 O LEU A 874 N PHE A 871 SHEET 3 AE 5 ARG A 948 ARG A 955 -1 O LYS A 951 N GLU A 879 SHEET 4 AE 5 MET A 986 SER A 993 -1 O VAL A 987 N LEU A 954 SHEET 5 AE 5 SER A 977 ASP A 981 -1 O SER A 977 N THR A 990 LINK O2 AGLA B 1 C1 FUC B 2 1555 1555 1.43 LINK O2 BGAL B 1 C1 FUC B 2 1555 1555 1.43 LINK O3 AGLA B 1 C1 AA2G B 3 1555 1555 1.36 LINK O3 BGAL B 1 C1 BA2G B 3 1555 1555 1.43 CISPEP 1 GLU A 710 HIS A 711 0 -12.54 CRYST1 92.250 154.020 96.660 90.00 90.00 90.00 C 2 2 21 8 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 0.010840 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010346 0.00000