HEADER SUGAR BINDING PROTEIN 07-SEP-10 2XQX TITLE STRUCTURE OF THE FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM TITLE 2 STREPTOCOCCUS PNEUMONIAE ENDOD COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CBM32, RESIDUES 804-948; COMPND 5 SYNONYM: ENDOD; COMPND 6 ENGINEERED: 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS SUGAR BINDING PROTEIN, CARBOHYDRATE BINDING, BETA-SANDWHICH EXPDTA X-RAY DIFFRACTION AUTHOR D.W.ABBOTT,A.B.BORASTON REVDAT 3 11-APR-12 2XQX 1 JRNL REMARK VERSN REVDAT 2 27-APR-11 2XQX 1 JRNL REVDAT 1 03-NOV-10 2XQX 0 JRNL AUTH D.W.ABBOTT,A.B.BORASTON JRNL TITL STRUCTURAL ANALYSIS OF A PUTATIVE FAMILY 32 JRNL TITL 2 CARBOHYDRATE-BINDING MODULE FROM THE STREPTOCOCCUS JRNL TITL 3 PNEUMONIAE ENZYME ENDOD. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 429 2011 JRNL REFN ISSN 1744-3091 JRNL PMID 21505233 JRNL DOI 10.1107/S1744309111001874 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 97.74 REMARK 3 NUMBER OF REFLECTIONS : 20817 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) : 0.21782 REMARK 3 R VALUE (WORKING SET) : 0.21537 REMARK 3 FREE R VALUE : 0.26216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1122 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) : 2.006 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.058 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1472 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.224 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.308 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2284 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.448 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31 REMARK 3 B22 (A**2) : 0.79 REMARK 3 B33 (A**2) : -1.13 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : -0.11 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.536 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2345 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3179 ; 1.256 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 293 ; 6.441 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;38.014 ;24.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 404 ;14.422 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.025 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 351 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1760 ; 0.005 ; 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): 1460 ; 0.605 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2346 ; 1.106 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 885 ; 1.683 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 832 ; 2.733 ; 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 2XQX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-SEP-10. REMARK 100 THE PDBE ID CODE IS EBI-45321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 20817 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 35.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 14.6 REMARK 200 R MERGE (I) : 0.14 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 14.3 REMARK 200 R MERGE FOR SHELL (I) : 0.31 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXC, SHELXD AND SHELXE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.05250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.05250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.75500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 GLY A 798 REMARK 465 SER A 799 REMARK 465 HIS A 800 REMARK 465 MSE A 801 REMARK 465 GLY B 798 REMARK 465 SER B 799 REMARK 465 HIS B 800 REMARK 465 MSE B 801 REMARK 465 ALA B 802 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 NH1 ARG A 902 OXT ACT B 1950 2.17 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 THR A 819 119.82 -162.58 REMARK 500 SER A 835 178.20 172.00 REMARK 500 ASP A 838 46.03 -91.31 REMARK 500 TRP A 935 75.02 -114.28 REMARK 500 SER B 835 -178.08 -176.40 REMARK 500 ASP B 838 43.94 -91.40 REMARK 500 ASP B 892 0.80 -69.95 REMARK 500 TRP B 935 74.26 -117.28 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 A1949 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 838 O REMARK 620 2 GLY A 827 O 90.0 REMARK 620 3 ASN A 830 OD1 126.7 70.7 REMARK 620 4 ASP A 838 OD1 66.7 82.1 61.8 REMARK 620 5 TYR A 941 O 85.6 87.8 139.6 150.3 REMARK 620 6 THR A 832 O 91.6 155.4 88.9 76.0 116.8 REMARK 620 7 ASN A 942 OD1 152.0 107.7 80.4 135.6 74.1 81.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1949 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR B 941 O REMARK 620 2 THR B 832 O 109.6 REMARK 620 3 ASP B 838 O 85.4 91.7 REMARK 620 4 ASN B 942 OD1 69.5 78.5 147.6 REMARK 620 5 GLY B 827 O 90.0 160.3 92.2 107.4 REMARK 620 6 ASN B 830 OD1 139.2 89.8 131.0 80.3 73.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1949 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B1949 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1951 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1951 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W92 RELATED DB: PDB REMARK 900 STRUCTURE OF A STREPTOCOCCUS PNEUMONIAE FAMILY REMARK 900 85 GLYCOSIDE HYDROLASE, ENDO-D, IN COMPLEX REMARK 900 WITH NAG-THIAZOLINE. REMARK 900 RELATED ID: 2W91 RELATED DB: PDB REMARK 900 STRUCTURE OF A STREPTOCOCCUS PNEUMONIAE FAMILY REMARK 900 85 GLYCOSIDE HYDROLASE, ENDO-D. DBREF 2XQX A 804 948 UNP Q93HW0 Q93HW0_STRPN 804 948 DBREF 2XQX B 804 948 UNP Q93HW0 Q93HW0_STRPN 804 948 SEQADV 2XQX GLY A 798 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX SER A 799 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX HIS A 800 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX MSE A 801 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX ALA A 802 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX SER A 803 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX GLY B 798 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX SER B 799 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX HIS B 800 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX MSE B 801 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX ALA B 802 UNP Q93HW0 EXPRESSION TAG SEQADV 2XQX SER B 803 UNP Q93HW0 EXPRESSION TAG SEQRES 1 A 151 GLY SER HIS MSE ALA SER ASN ILE VAL PRO GLY ALA THR SEQRES 2 A 151 VAL ILE ASP SER THR PHE PRO LYS THR GLU GLY GLY GLU SEQRES 3 A 151 GLY ILE GLU GLY MSE LEU ASN GLY THR ILE THR SER LEU SEQRES 4 A 151 SER ASP LYS TRP SER SER ALA GLN LEU SER GLY SER VAL SEQRES 5 A 151 ASP ILE ARG LEU THR LYS PRO ARG THR VAL VAL ARG TRP SEQRES 6 A 151 VAL MSE ASP HIS ALA GLY ALA GLY GLY GLU SER VAL ASN SEQRES 7 A 151 ASP GLY LEU MSE ASN THR LYS ASP PHE ASP LEU TYR TYR SEQRES 8 A 151 LYS ASP ALA ASP GLY GLU TRP LYS LEU ALA LYS GLU VAL SEQRES 9 A 151 ARG GLY ASN LYS ALA HIS VAL THR ASP ILE THR LEU ASP SEQRES 10 A 151 LYS PRO ILE THR ALA GLN ASP TRP ARG LEU ASN VAL VAL SEQRES 11 A 151 THR SER ASP ASN GLY THR PRO TRP LYS ALA ILE ARG ILE SEQRES 12 A 151 TYR ASN TRP LYS MSE TYR GLU LYS SEQRES 1 B 151 GLY SER HIS MSE ALA SER ASN ILE VAL PRO GLY ALA THR SEQRES 2 B 151 VAL ILE ASP SER THR PHE PRO LYS THR GLU GLY GLY GLU SEQRES 3 B 151 GLY ILE GLU GLY MSE LEU ASN GLY THR ILE THR SER LEU SEQRES 4 B 151 SER ASP LYS TRP SER SER ALA GLN LEU SER GLY SER VAL SEQRES 5 B 151 ASP ILE ARG LEU THR LYS PRO ARG THR VAL VAL ARG TRP SEQRES 6 B 151 VAL MSE ASP HIS ALA GLY ALA GLY GLY GLU SER VAL ASN SEQRES 7 B 151 ASP GLY LEU MSE ASN THR LYS ASP PHE ASP LEU TYR TYR SEQRES 8 B 151 LYS ASP ALA ASP GLY GLU TRP LYS LEU ALA LYS GLU VAL SEQRES 9 B 151 ARG GLY ASN LYS ALA HIS VAL THR ASP ILE THR LEU ASP SEQRES 10 B 151 LYS PRO ILE THR ALA GLN ASP TRP ARG LEU ASN VAL VAL SEQRES 11 B 151 THR SER ASP ASN GLY THR PRO TRP LYS ALA ILE ARG ILE SEQRES 12 B 151 TYR ASN TRP LYS MSE TYR GLU LYS MODRES 2XQX MSE A 828 MET SELENOMETHIONINE MODRES 2XQX MSE A 864 MET SELENOMETHIONINE MODRES 2XQX MSE A 879 MET SELENOMETHIONINE MODRES 2XQX MSE A 945 MET SELENOMETHIONINE MODRES 2XQX MSE B 828 MET SELENOMETHIONINE MODRES 2XQX MSE B 864 MET SELENOMETHIONINE MODRES 2XQX MSE B 879 MET SELENOMETHIONINE MODRES 2XQX MSE B 945 MET SELENOMETHIONINE HET MSE A 828 8 HET MSE A 864 8 HET MSE A 879 8 HET MSE A 945 8 HET MSE B 828 8 HET MSE B 864 8 HET MSE B 879 8 HET MSE B 945 8 HET CA A1949 1 HET CA B1949 1 HET ACT B1950 4 HET ACT A1950 4 HET ACT B1951 4 HET ACT A1951 4 HETNAM MSE SELENOMETHIONINE HETNAM ACT ACETATE ION HETNAM CA CALCIUM ION FORMUL 3 MSE 8(C5 H11 N O2 SE) FORMUL 4 ACT 4(C2 H3 O2 1-) FORMUL 5 CA 2(CA 2+) FORMUL 6 HOH *288(H2 O) HELIX 1 1 GLY A 824 LEU A 829 5 6 HELIX 2 2 GLY A 868 GLY A 871 5 4 HELIX 3 3 GLY B 824 LEU B 829 5 6 HELIX 4 4 ALA B 867 GLY B 871 5 5 SHEET 1 AA 2 THR A 810 SER A 814 0 SHEET 2 AA 2 GLY A 847 HIS A 866 -1 O ASP A 850 N ILE A 812 SHEET 1 AB 6 TRP A 840 SER A 842 0 SHEET 2 AB 6 ILE A 938 TYR A 946 -1 O ILE A 938 N SER A 842 SHEET 3 AB 6 GLY A 847 HIS A 866 -1 N VAL A 860 O TYR A 946 SHEET 4 AB 6 VAL A 908 THR A 928 -1 O THR A 909 N MSE A 864 SHEET 5 AB 6 ASP A 883 LYS A 889 -1 O ASP A 883 N VAL A 927 SHEET 6 AB 6 TRP A 895 VAL A 901 -1 O LYS A 896 N TYR A 888 SHEET 1 AC 4 TRP A 840 SER A 842 0 SHEET 2 AC 4 ILE A 938 TYR A 946 -1 O ILE A 938 N SER A 842 SHEET 3 AC 4 GLY A 847 HIS A 866 -1 N VAL A 860 O TYR A 946 SHEET 4 AC 4 THR A 810 SER A 814 -1 O THR A 810 N ARG A 852 SHEET 1 BA 2 THR B 810 SER B 814 0 SHEET 2 BA 2 GLY B 847 ASP B 865 -1 O ASP B 850 N ILE B 812 SHEET 1 BB 5 TRP B 895 VAL B 901 0 SHEET 2 BB 5 ASP B 883 LYS B 889 -1 O PHE B 884 N VAL B 901 SHEET 3 BB 5 VAL B 908 THR B 928 -1 O ASP B 921 N LYS B 889 SHEET 4 BB 5 GLY B 847 ASP B 865 -1 O GLY B 847 N VAL B 926 SHEET 5 BB 5 ASN B 942 TYR B 946 1 O ASN B 942 N ASP B 865 SHEET 1 BC 5 TRP B 895 VAL B 901 0 SHEET 2 BC 5 ASP B 883 LYS B 889 -1 O PHE B 884 N VAL B 901 SHEET 3 BC 5 VAL B 908 THR B 928 -1 O ASP B 921 N LYS B 889 SHEET 4 BC 5 GLY B 847 ASP B 865 -1 O GLY B 847 N VAL B 926 SHEET 5 BC 5 THR B 810 SER B 814 -1 O THR B 810 N ARG B 852 SHEET 1 BD 2 ASN B 942 TYR B 946 0 SHEET 2 BD 2 GLY B 847 ASP B 865 1 N VAL B 860 O TYR B 946 SHEET 1 BE 2 TRP B 840 SER B 842 0 SHEET 2 BE 2 ILE B 938 ILE B 940 -1 O ILE B 938 N SER B 842 LINK C GLY A 827 N MSE A 828 1555 1555 1.33 LINK C MSE A 828 N LEU A 829 1555 1555 1.33 LINK C VAL A 863 N MSE A 864 1555 1555 1.33 LINK C MSE A 864 N ASP A 865 1555 1555 1.34 LINK C LEU A 878 N MSE A 879 1555 1555 1.32 LINK C MSE A 879 N ASN A 880 1555 1555 1.33 LINK C LYS A 944 N MSE A 945 1555 1555 1.32 LINK C MSE A 945 N TYR A 946 1555 1555 1.32 LINK CA CA A1949 O THR A 832 1555 1555 2.38 LINK CA CA A1949 O TYR A 941 1555 1555 2.33 LINK CA CA A1949 OD1 ASP A 838 1555 1555 2.88 LINK CA CA A1949 OD1 ASN A 830 1555 1555 2.65 LINK CA CA A1949 O GLY A 827 1555 1555 2.49 LINK CA CA A1949 O ASP A 838 1555 1555 2.55 LINK CA CA A1949 OD1 ASN A 942 1555 1555 2.70 LINK C GLY B 827 N MSE B 828 1555 1555 1.33 LINK C MSE B 828 N LEU B 829 1555 1555 1.33 LINK C VAL B 863 N MSE B 864 1555 1555 1.33 LINK C MSE B 864 N ASP B 865 1555 1555 1.34 LINK C LEU B 878 N MSE B 879 1555 1555 1.32 LINK C MSE B 879 N ASN B 880 1555 1555 1.33 LINK C LYS B 944 N MSE B 945 1555 1555 1.33 LINK C MSE B 945 N TYR B 946 1555 1555 1.33 LINK CA CA B1949 O THR B 832 1555 1555 2.51 LINK CA CA B1949 O ASP B 838 1555 1555 2.56 LINK CA CA B1949 OD1 ASN B 942 1555 1555 2.75 LINK CA CA B1949 O GLY B 827 1555 1555 2.38 LINK CA CA B1949 OD1 ASN B 830 1555 1555 2.47 LINK CA CA B1949 O TYR B 941 1555 1555 2.40 CISPEP 1 GLU A 820 GLY A 821 0 4.12 SITE 1 AC1 6 GLY A 827 ASN A 830 THR A 832 ASP A 838 SITE 2 AC1 6 TYR A 941 ASN A 942 SITE 1 AC2 6 GLY B 827 ASN B 830 THR B 832 ASP B 838 SITE 2 AC2 6 TYR B 941 ASN B 942 SITE 1 AC3 3 ARG A 902 ALA B 843 GLN B 844 SITE 1 AC4 3 GLY A 868 VAL A 874 GLY B 903 SITE 1 AC5 5 GLY A 903 GLY B 868 GLY B 871 VAL B 874 SITE 2 AC5 5 HOH B2133 SITE 1 AC6 2 HOH A2096 HOH A2122 CRYST1 134.105 73.510 34.597 90.00 96.52 90.00 C 1 2 1 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 0.007457 0.000000 0.000852 0.00000 SCALE2 0.000000 0.013604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029092 0.00000