HEADER HYDROLASE 31-MAY-11 2YL8
TITLE INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND
TITLE 2 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND
TITLE 3 HYDROLYSIS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-N-ACETYLHEXOSAMINIDASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 181-614;
COMPND 5 SYNONYM: GLYCOSIDE HYDROLASE GH20;
COMPND 6 EC: 3.2.1.52;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE;
SOURCE 3 ORGANISM_TAXID: 170187;
SOURCE 4 STRAIN: TIGR4;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28A
KEYWDS HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR B.PLUVINAGE,M.A.HIGGINS,D.W.ABBOTT,C.ROBB,A.B.DALIA,L.DENG,
AUTHOR 2 J.N.WEISER,T.B.PARSONS,A.J.FAIRBANKS,D.J.VOCADLO,A.B.BORASTON
REVDAT 2 23-NOV-11 2YL8 1 AUTHOR JRNL REMARK
REVDAT 1 07-SEP-11 2YL8 0
JRNL AUTH B.PLUVINAGE,M.A.HIGGINS,D.W.ABBOTT,C.ROBB,A.B.DALIA,L.DENG,
JRNL AUTH 2 J.N.WEISER,T.B.PARSONS,A.J.FAIRBANKS,D.J.VOCADLO,
JRNL AUTH 3 A.B.BORASTON
JRNL TITL INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND
JRNL TITL 2 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS.
JRNL TITL 3
JRNL REF STRUCTURE V. 19 1603 2011
JRNL REFN ISSN 0969-2126
JRNL PMID 22078560
JRNL DOI 10.1016/J.STR.2011.08.011
REMARK 2
REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0072
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.60
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.95
REMARK 3 NUMBER OF REFLECTIONS : 46762
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) : 0.16647
REMARK 3 R VALUE (WORKING SET) : 0.16444
REMARK 3 FREE R VALUE : 0.20522
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1
REMARK 3 FREE R VALUE TEST SET COUNT : 2491
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) : 1.750
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.795
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3397
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00
REMARK 3 BIN R VALUE (WORKING SET) : 0.211
REMARK 3 BIN FREE R VALUE SET COUNT : 215
REMARK 3 BIN FREE R VALUE : 0.282
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3571
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 72
REMARK 3 SOLVENT ATOMS : 648
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.374
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.13
REMARK 3 B22 (A**2) : -0.16
REMARK 3 B33 (A**2) : 0.03
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.112
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.032
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3729 ; 0.015 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5073 ; 1.425 ; 1.972
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 483 ; 5.820 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;36.988 ;25.549
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 634 ;12.641 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.347 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 543 ; 0.094 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2883 ; 0.007 ; 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): 2264 ; 0.733 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3654 ; 1.290 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1465 ; 2.361 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1406 ; 3.903 ; 4.500
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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
REMARK 3 RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
REMARK 4
REMARK 4 2YL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-11.
REMARK 100 THE PDBE ID CODE IS EBI-48501.
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 : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL9-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD (MX-325)
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49280
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.75
REMARK 200 RESOLUTION RANGE LOW (A) : 35.60
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 8.0
REMARK 200 R MERGE (I) : 0.09
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.40
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 8.0
REMARK 200 R MERGE FOR SHELL (I) : 0.40
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.40
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.08
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
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+1/2
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 0.00000
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 0.00000
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 39.28500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.64500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.46500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.28500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.64500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.46500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.28500
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.64500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.46500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.28500
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.64500
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.46500
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 MN MN A1620 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2382 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2384 LIES ON A SPECIAL POSITION.
REMARK 400
REMARK 400 COMPOUND
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 361 TO GLN
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 LYS A 370 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 OD1 ASN A 364 O HOH A 2314 2.08
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 ASN A 225 93.40 -161.16
REMARK 500 ASP A 226 -75.12 69.95
REMARK 500 TYR A 261 117.07 -162.81
REMARK 500 LYS A 350 -23.62 71.73
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED
REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND ARE
REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL
REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE): THESE HAVE BEEN REPOSITIONED
REMARK 525 BY APPLYING THE SYMMETRY TRANSFORMATION INDICATED.
REMARK 525
REMARK 525 M RES CSSEQI ORIGINAL COORDINATES SYMMETRY TRANS. DIST.
REMARK 525 X Y Z
REMARK 525 HOH A2103 30.921 20.443 24.444 008 455 3.45
REMARK 525 HOH A2238 26.582 26.133 27.688 008 455 3.29
REMARK 525 HOH A2228 31.187 17.226 24.919 008 455 3.33
REMARK 525 HOH A2250 34.471 34.826 25.138 008 455 3.58
REMARK 525 HOH A2298 9.699 88.691 0.462 004 565 2.72
REMARK 525 HOH A2297 29.571 89.201 1.671 004 565 2.57
REMARK 525 HOH A2328 23.140 88.734 14.774 007 545 2.62
REMARK 525 HOH A2138 9.659 0.372 29.420 007 555 4.25
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 POLYETHYLENE GLYCOL (15P): (N=34)
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 15P A 1624
REMARK 610 15P A 1625
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 MN A1615 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 329 OD2
REMARK 620 2 HOH A2259 O 87.0
REMARK 620 3 HOH A2257 O 84.3 169.0
REMARK 620 4 HOH A2258 O 91.7 88.2 85.5
REMARK 620 5 HOH A2260 O 86.1 92.0 94.0 177.8
REMARK 620 6 HOH A2359 O 178.3 92.3 96.6 89.8 92.4
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1616 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 485 OD2
REMARK 620 2 HOH A2455 O 88.4
REMARK 620 3 HOH A2466 O 90.8 84.1
REMARK 620 4 ASP A 477 OD1 96.2 96.8 173.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1617 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 422 OD1
REMARK 620 2 HOH A2394 O 89.0
REMARK 620 3 HOH A2393 O 96.4 132.1
REMARK 620 4 HOH A2640 O 144.7 81.8 66.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1618 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2127 O
REMARK 620 2 ASP A 259 OD2 86.5
REMARK 620 3 HOH A2126 O 89.4 92.1
REMARK 620 4 HOH A2641 O 92.0 177.7 86.0
REMARK 620 5 HOH A2124 O 174.2 87.9 92.3 93.6
REMARK 620 6 HOH A2128 O 91.6 85.1 177.0 96.7 86.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1619 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2642 O
REMARK 620 2 HOH A2089 O 98.6
REMARK 620 3 ASP A 247 OD2 177.0 83.5
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1620 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 585 OD2
REMARK 620 2 ASP A 585 OD2 157.2
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1621 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 553 OE1
REMARK 620 2 GLU A 550 OE1 94.1
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1622 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2051 O
REMARK 620 2 GLU A 550 OE2 74.0
REMARK 620 N 1
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1615
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1616
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1617
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1618
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1619
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1620
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1621
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1622
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1623
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A1624
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A1625
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A1626
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A1627
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1628
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2YL9 RELATED DB: PDB
REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND
REMARK 900 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
REMARK 900 RELATED ID: 2YLA RELATED DB: PDB
REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND
REMARK 900 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
REMARK 900 RELATED ID: 2YL6 RELATED DB: PDB
REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND
REMARK 900 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
REMARK 900 RELATED ID: 2YL5 RELATED DB: PDB
REMARK 900 INHIBITION OF THE PNEUMOCCOCAL VIRULENCE FACTOR STRH AND
REMARK 900 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
REMARK 900 RELATED ID: 2YLL RELATED DB: PDB
REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND
REMARK 900 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND
REMARK 900 HYDROLYSIS
DBREF 2YL8 A 181 614 UNP P49610 STRH_STRPN 181 614
SEQADV 2YL8 GLN A 361 UNP P49610 GLU 361 ENGINEERED MUTATION
SEQRES 1 A 434 ASN GLU LYS LEU ALA LYS LYS LYS ILE VAL SER ILE ASP
SEQRES 2 A 434 ALA GLY ARG LYS TYR PHE SER PRO GLU GLN LEU LYS GLU
SEQRES 3 A 434 ILE ILE ASP LYS ALA LYS HIS TYR GLY TYR THR ASP LEU
SEQRES 4 A 434 HIS LEU LEU VAL GLY ASN ASP GLY LEU ARG PHE MET LEU
SEQRES 5 A 434 ASP ASP MET SER ILE THR ALA ASN GLY LYS THR TYR ALA
SEQRES 6 A 434 SER ASP ASP VAL LYS ARG ALA ILE GLU LYS GLY THR ASN
SEQRES 7 A 434 ASP TYR TYR ASN ASP PRO ASN GLY ASN HIS LEU THR GLU
SEQRES 8 A 434 SER GLN MET THR ASP LEU ILE ASN TYR ALA LYS ASP LYS
SEQRES 9 A 434 GLY ILE GLY LEU ILE PRO THR VAL ASN SER PRO GLY HIS
SEQRES 10 A 434 MET ASP ALA ILE LEU ASN ALA MET LYS GLU LEU GLY ILE
SEQRES 11 A 434 GLN ASN PRO ASN PHE SER TYR PHE GLY LYS LYS SER ALA
SEQRES 12 A 434 ARG THR VAL ASP LEU ASP ASN GLU GLN ALA VAL ALA PHE
SEQRES 13 A 434 THR LYS ALA LEU ILE ASP LYS TYR ALA ALA TYR PHE ALA
SEQRES 14 A 434 LYS LYS THR GLU ILE PHE ASN ILE GLY LEU ASP GLN TYR
SEQRES 15 A 434 ALA ASN ASP ALA THR ASP ALA LYS GLY TRP SER VAL LEU
SEQRES 16 A 434 GLN ALA ASP LYS TYR TYR PRO ASN GLU GLY TYR PRO VAL
SEQRES 17 A 434 LYS GLY TYR GLU LYS PHE ILE ALA TYR ALA ASN ASP LEU
SEQRES 18 A 434 ALA ARG ILE VAL LYS SER HIS GLY LEU LYS PRO MET ALA
SEQRES 19 A 434 PHE ASN ASP GLY ILE TYR TYR ASN SER ASP THR SER PHE
SEQRES 20 A 434 GLY SER PHE ASP LYS ASP ILE ILE VAL SER MET TRP THR
SEQRES 21 A 434 GLY GLY TRP GLY GLY TYR ASP VAL ALA SER SER LYS LEU
SEQRES 22 A 434 LEU ALA GLU LYS GLY HIS GLN ILE LEU ASN THR ASN ASP
SEQRES 23 A 434 ALA TRP TYR TYR VAL LEU GLY ARG ASN ALA ASP GLY GLN
SEQRES 24 A 434 GLY TRP TYR ASN LEU ASP GLN GLY LEU ASN GLY ILE LYS
SEQRES 25 A 434 ASN THR PRO ILE THR SER VAL PRO LYS THR GLU GLY ALA
SEQRES 26 A 434 ASP ILE PRO ILE ILE GLY GLY MET VAL ALA ALA TRP ALA
SEQRES 27 A 434 ASP THR PRO SER ALA ARG TYR SER PRO SER ARG LEU PHE
SEQRES 28 A 434 LYS LEU MET ARG HIS PHE ALA ASN ALA ASN ALA GLU TYR
SEQRES 29 A 434 PHE ALA ALA ASP TYR GLU SER ALA GLU GLN ALA LEU ASN
SEQRES 30 A 434 GLU VAL PRO LYS ASP LEU ASN ARG TYR THR ALA GLU SER
SEQRES 31 A 434 VAL THR ALA VAL LYS GLU ALA GLU LYS ALA ILE ARG SER
SEQRES 32 A 434 LEU ASP SER ASN LEU SER ARG ALA GLN GLN ASP THR ILE
SEQRES 33 A 434 ASP GLN ALA ILE ALA LYS LEU GLN GLU THR VAL ASN ASN
SEQRES 34 A 434 LEU THR LEU THR PRO
HET MN A1615 1
HET MN A1616 1
HET MN A1617 1
HET MN A1618 1
HET MN A1619 1
HET MN A1620 1
HET MN A1621 1
HET MN A1622 1
HET MN A1623 1
HET 15P A1624 24
HET 15P A1625 9
HET NAG A1626 14
HET MAN A1627 12
HET EDO A1628 4
HETNAM MN MANGANESE (II) ION
HETNAM 15P POLYETHYLENE GLYCOL (N=34)
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETNAM MAN ALPHA-D-MANNOSE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN 15P PEG 1500
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 MN 9(MN 2+)
FORMUL 3 15P 2(C69 H140 O35)
FORMUL 4 NAG C8 H15 N O6
FORMUL 5 MAN C6 H12 O6
FORMUL 6 EDO C2 H6 O2
FORMUL 7 HOH *648(H2 O)
HELIX 1 1 SER A 200 GLY A 215 1 16
HELIX 2 2 ALA A 245 TYR A 261 1 17
HELIX 3 3 GLU A 271 LYS A 284 1 14
HELIX 4 4 MET A 298 GLY A 309 1 12
HELIX 5 5 ASN A 330 ALA A 349 1 20
HELIX 6 6 ALA A 363 ASP A 368 1 6
HELIX 7 7 LYS A 370 TYR A 381 1 12
HELIX 8 8 LYS A 389 HIS A 408 1 20
HELIX 9 9 TYR A 420 ASP A 424 5 5
HELIX 10 10 SER A 450 LYS A 457 1 8
HELIX 11 11 ASN A 465 TYR A 469 5 5
HELIX 12 12 ASN A 483 THR A 494 1 12
HELIX 13 13 SER A 526 ASN A 541 1 16
HELIX 14 14 TYR A 549 GLU A 558 1 10
HELIX 15 15 THR A 567 SER A 583 1 17
HELIX 16 16 GLN A 592 ASN A 609 1 18
SHEET 1 1 1 LYS A 187 ASP A 193 0
SHEET 2 2 1 ASP A 218 GLY A 224 0
SHEET 3 3 1 PHE A 230 MET A 231 0
SHEET 4 4 1 ILE A 237 ALA A 239 0
SHEET 5 5 1 LYS A 242 TYR A 244 0
SHEET 6 6 1 LEU A 269 THR A 270 0
SHEET 7 7 1 GLY A 287 SER A 294 0
SHEET 8 8 1 ASN A 314 TYR A 317 0
SHEET 9 9 1 LYS A 320 VAL A 326 0
SHEET 10 10 1 ILE A 354 GLY A 358 0
SHEET 11 11 1 LYS A 411 PHE A 415 0
SHEET 12 12 1 ILE A 435 MET A 438 0
SHEET 13 13 1 ILE A 461 ASN A 463 0
SHEET 14 14 1 TYR A 470 VAL A 471 0
SHEET 15 15 1 GLY A 511 TRP A 517 0
LINK MN MN A1615 OD2 ASP A 329 1555 1555 2.20
LINK MN MN A1615 O HOH A2259 1555 1555 2.27
LINK MN MN A1615 O HOH A2257 1555 1555 2.24
LINK MN MN A1615 O HOH A2258 1555 1555 2.17
LINK MN MN A1615 O HOH A2260 1555 1555 2.14
LINK MN MN A1615 O HOH A2359 1555 1555 2.26
LINK MN MN A1616 OD2 ASP A 485 1555 1555 2.20
LINK MN MN A1616 O HOH A2455 1555 1555 2.21
LINK MN MN A1616 O HOH A2466 1555 1555 2.08
LINK MN MN A1616 OD1 ASP A 477 1555 1555 2.29
LINK MN MN A1617 OD1 ASN A 422 1555 1555 2.11
LINK MN MN A1617 O HOH A2394 1555 1555 2.38
LINK MN MN A1617 O HOH A2393 1555 1555 2.18
LINK MN MN A1617 O HOH A2640 1555 1555 2.62
LINK MN MN A1618 O HOH A2641 1555 1555 2.15
LINK MN MN A1618 OD2 ASP A 259 1555 1555 2.13
LINK MN MN A1618 O HOH A2126 1555 1555 2.24
LINK MN MN A1618 O HOH A2124 1555 1555 2.17
LINK MN MN A1618 O HOH A2128 1555 1555 2.26
LINK MN MN A1618 O HOH A2127 1555 1555 2.12
LINK MN MN A1619 O HOH A2089 1555 1555 2.42
LINK MN MN A1619 OD2AASP A 247 1555 1555 2.27
LINK MN MN A1619 O HOH A2642 1555 1555 2.34
LINK MN MN A1620 OD2 ASP A 585 1555 4565 2.18
LINK MN MN A1620 OD2 ASP A 585 1555 1555 2.18
LINK MN MN A1621 OE1 GLU A 550 1555 1555 2.24
LINK MN MN A1621 OE1 GLU A 553 1555 1555 2.15
LINK MN MN A1622 OE2 GLU A 550 1555 1555 2.29
LINK MN MN A1622 O HOH A2051 1555 1555 2.27
LINK MN MN A1623 O HOH A2645 1555 1555 2.36
LINK C1 NAG A1626 O2 MAN A1627 1555 1555 1.43
CISPEP 1 SER A 294 PRO A 295 0 -5.63
SITE 1 AC1 6 ASP A 329 HOH A2257 HOH A2258 HOH A2259
SITE 2 AC1 6 HOH A2260 HOH A2359
SITE 1 AC2 4 ASP A 477 ASP A 485 HOH A2455 HOH A2466
SITE 1 AC3 5 ASN A 422 ASP A 447 HOH A2393 HOH A2394
SITE 2 AC3 5 HOH A2640
SITE 1 AC4 6 ASP A 259 HOH A2124 HOH A2126 HOH A2127
SITE 2 AC4 6 HOH A2128 HOH A2641
SITE 1 AC5 4 ASP A 247 ASN A 608 HOH A2089 HOH A2642
SITE 1 AC6 1 ASP A 585
SITE 1 AC7 5 GLU A 550 GLU A 553 MN A1622 MN A1623
SITE 2 AC7 5 HOH A2548
SITE 1 AC8 4 GLU A 550 MN A1621 HOH A2051 HOH A2544
SITE 1 AC9 4 GLU A 550 MN A1621 HOH A2548 HOH A2645
SITE 1 BC1 8 TYR A 317 PHE A 318 SER A 373 TYR A 381
SITE 2 BC1 8 TYR A 386 HOH A2236 HOH A2335 HOH A2646
SITE 1 BC2 2 ASN A 422 ASP A 424
SITE 1 BC3 13 ARG A 196 HIS A 297 ASP A 360 GLN A 361
SITE 2 BC3 13 PHE A 415 TRP A 439 TYR A 469 TYR A 482
SITE 3 BC3 13 TRP A 517 ASP A 519 MAN A1627 HOH A2061
SITE 4 BC3 13 HOH A2449
SITE 1 BC4 10 GLN A 361 ASN A 364 TRP A 443 TYR A 482
SITE 2 BC4 10 ASP A 519 NAG A1626 HOH A2022 HOH A2314
SITE 3 BC4 10 HOH A2465 HOH A2648
SITE 1 BC5 7 PHE A 315 ASP A 327 LEU A 328 ASP A 329
SITE 2 BC5 7 TYR A 362 LEU A 375 HOH A2260
CRYST1 78.570 109.290 112.930 90.00 90.00 90.00 I 2 2 2 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 0.012728 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009150 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008855 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
