HEADER HYDROLASE 28-MAY-12 2LTJ TITLE CONFORMATIONAL ANALYSIS OF STRH, THE SURFACE-ATTACHED EXO- BETA-D-N- TITLE 2 ACETYLGLUCOSAMINIDASE FROM STREPTOCOCCUS PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-N-ACETYLHEXOSAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: G5 1 DOMAIN RESIDUES 1050-1140; COMPND 5 EC: 3.2.1.52; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: STRH, SP_0057; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET-28A KEYWDS ELONGATED, B-SHEET, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR B.PLUVINAGE,S.CHITAYAT,E.FICKO-BLEAN,D.ABBOTT,J.KUNJACHEN,J.GRONDIN, AUTHOR 2 H.SPENCER,S.SMITH,A.BORASTON REVDAT 2 19-JUN-13 2LTJ 1 JRNL REVDAT 1 28-NOV-12 2LTJ 0 JRNL AUTH B.PLUVINAGE,S.CHITAYAT,E.FICKO-BLEAN,D.W.ABBOTT, JRNL AUTH 2 J.M.KUNJACHEN,J.GRONDIN,H.L.SPENCER,S.P.SMITH,A.B.BORASTON JRNL TITL CONFORMATIONAL ANALYSIS OF STRH, THE SURFACE-ATTACHED JRNL TITL 2 EXO-BETA-D-N-ACETYLGLUCOSAMINIDASE FROM STREPTOCOCCUS JRNL TITL 3 PNEUMONIAE. JRNL REF J.MOL.BIOL. V. 425 334 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23154168 JRNL DOI 10.1016/J.JMB.2012.11.005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THERE WERE NO RESTRAINTS FOR THE HIS- REMARK 3 TAG REGION OF THE PROTEIN. REMARK 4 REMARK 4 2LTJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-12. REMARK 100 THE RCSB ID CODE IS RCSB102815. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.025 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 G5, 25 MM TRIS, 25 MM SODIUM REMARK 210 CHLORIDE, 0.5 MM DSS, 1 MM DTT, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 3D C(CO)NH; 3D HNCACB; 3D H(CCO) REMARK 210 NH; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, VNMRJ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-21 REMARK 465 RES C SSSEQI REMARK 465 HIS A 4A REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 2 HIS A 7 CB HIS A 7 CG 0.212 REMARK 500 2 HIS A 7 CG HIS A 7 CD2 0.138 REMARK 500 2 HIS A 7 CG HIS A 7 ND1 0.187 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 HIS A 7 CB - CG - CD2 ANGL. DEV. = 22.8 DEGREES REMARK 500 2 HIS A 7 ND1 - CG - CD2 ANGL. DEV. = -73.4 DEGREES REMARK 500 2 HIS A 7 CG - ND1 - CE1 ANGL. DEV. = -72.8 DEGREES REMARK 500 2 HIS A 7 ND1 - CE1 - NE2 ANGL. DEV. = -73.0 DEGREES REMARK 500 2 HIS A 7 CE1 - NE2 - CD2 ANGL. DEV. = -70.1 DEGREES REMARK 500 2 HIS A 7 CG - CD2 - NE2 ANGL. DEV. = -63.2 DEGREES 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 1 HIS A 6 34.92 -147.90 REMARK 500 1 HIS A 8 31.53 -160.92 REMARK 500 1 HIS A 9 37.34 -175.65 REMARK 500 1 LEU A 13 -68.94 -99.50 REMARK 500 1 PRO A 15 -71.54 -58.57 REMARK 500 1 ASN A 25 32.49 -145.26 REMARK 500 1 ALA A 28 -75.47 -130.29 REMARK 500 1 ALA A 29 36.48 -174.15 REMARK 500 1 ASN A 30 175.73 59.93 REMARK 500 1 GLU A 32 -76.65 -166.42 REMARK 500 1 THR A 33 -48.95 -164.30 REMARK 500 1 PRO A 35 -165.75 -66.55 REMARK 500 1 ARG A 40 112.96 -174.01 REMARK 500 1 PRO A 57 43.39 -80.84 REMARK 500 1 ALA A 58 142.07 61.88 REMARK 500 1 THR A 65 100.35 -166.56 REMARK 500 1 LEU A 90 -56.72 -149.18 REMARK 500 1 LYS A 96 48.75 107.53 REMARK 500 1 GLU A 97 122.24 -33.72 REMARK 500 1 PRO A 108 -73.25 -59.09 REMARK 500 1 VAL A 109 -45.19 -178.53 REMARK 500 1 THR A 110 38.00 -177.83 REMARK 500 2 SER A 3 87.87 -158.58 REMARK 500 2 HIS A 6 175.36 63.98 REMARK 500 2 HIS A 7 -150.24 -78.64 REMARK 500 2 HIS A 9 178.02 61.56 REMARK 500 2 SER A 10 56.44 -119.46 REMARK 500 2 LEU A 13 -45.00 -155.04 REMARK 500 2 VAL A 14 86.89 -150.19 REMARK 500 2 SER A 18 -157.39 60.38 REMARK 500 2 MET A 20 113.66 71.34 REMARK 500 2 ASN A 25 157.56 73.45 REMARK 500 2 GLU A 26 -92.38 70.98 REMARK 500 2 VAL A 27 -55.45 -176.75 REMARK 500 2 ALA A 28 -96.76 33.62 REMARK 500 2 GLU A 43 97.82 -65.86 REMARK 500 2 PRO A 57 -74.12 -60.77 REMARK 500 2 ALA A 58 122.51 -178.76 REMARK 500 2 LYS A 84 108.07 -162.13 REMARK 500 2 LEU A 90 -83.94 -137.64 REMARK 500 2 THR A 95 72.08 -117.61 REMARK 500 2 LYS A 96 -43.57 149.37 REMARK 500 2 GLU A 97 115.32 64.55 REMARK 500 2 GLN A 101 98.46 -59.64 REMARK 500 2 THR A 110 123.05 176.68 REMARK 500 3 SER A 3 36.33 -163.45 REMARK 500 3 HIS A 7 88.95 59.32 REMARK 500 3 HIS A 8 30.43 -161.74 REMARK 500 3 HIS A 9 82.39 58.96 REMARK 500 3 SER A 10 -75.88 -88.79 REMARK 500 REMARK 500 THIS ENTRY HAS 480 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 HIS A 7 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18484 RELATED DB: BMRB DBREF 2LTJ A 21 111 UNP P49610 STRH_STRPN 1050 1140 SEQADV 2LTJ MET A 1 UNP P49610 EXPRESSION TAG SEQADV 2LTJ GLY A 2 UNP P49610 EXPRESSION TAG SEQADV 2LTJ SER A 3 UNP P49610 EXPRESSION TAG SEQADV 2LTJ SER A 4 UNP P49610 EXPRESSION TAG SEQADV 2LTJ HIS A 4A UNP P49610 EXPRESSION TAG SEQADV 2LTJ HIS A 5 UNP P49610 EXPRESSION TAG SEQADV 2LTJ HIS A 6 UNP P49610 EXPRESSION TAG SEQADV 2LTJ HIS A 7 UNP P49610 EXPRESSION TAG SEQADV 2LTJ HIS A 8 UNP P49610 EXPRESSION TAG SEQADV 2LTJ HIS A 9 UNP P49610 EXPRESSION TAG SEQADV 2LTJ SER A 10 UNP P49610 EXPRESSION TAG SEQADV 2LTJ SER A 11 UNP P49610 EXPRESSION TAG SEQADV 2LTJ GLY A 12 UNP P49610 EXPRESSION TAG SEQADV 2LTJ LEU A 13 UNP P49610 EXPRESSION TAG SEQADV 2LTJ VAL A 14 UNP P49610 EXPRESSION TAG SEQADV 2LTJ PRO A 15 UNP P49610 EXPRESSION TAG SEQADV 2LTJ ARG A 16 UNP P49610 EXPRESSION TAG SEQADV 2LTJ GLY A 17 UNP P49610 EXPRESSION TAG SEQADV 2LTJ SER A 18 UNP P49610 EXPRESSION TAG SEQADV 2LTJ HIS A 19 UNP P49610 EXPRESSION TAG SEQADV 2LTJ MET A 20 UNP P49610 EXPRESSION TAG SEQRES 1 A 112 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 112 LEU VAL PRO ARG GLY SER HIS MET SER LEU ASP GLU ASN SEQRES 3 A 112 GLU VAL ALA ALA ASN VAL GLU THR ARG PRO GLU LEU ILE SEQRES 4 A 112 THR ARG THR GLU GLU ILE PRO PHE GLU VAL ILE LYS LYS SEQRES 5 A 112 GLU ASN PRO ASN LEU PRO ALA GLY GLN GLU ASN ILE ILE SEQRES 6 A 112 THR ALA GLY VAL LYS GLY GLU ARG THR HIS TYR ILE SER SEQRES 7 A 112 VAL LEU THR GLU ASN GLY LYS THR THR GLU THR VAL LEU SEQRES 8 A 112 ASP SER GLN VAL THR LYS GLU VAL ILE ASN GLN VAL VAL SEQRES 9 A 112 GLU VAL GLY ALA PRO VAL THR HIS SHEET 1 A 3 GLU A 36 ILE A 44 0 SHEET 2 A 3 GLY A 70 THR A 80 -1 O ILE A 76 N ILE A 38 SHEET 3 A 3 THR A 85 THR A 86 -1 N THR A 86 O LEU A 79 SHEET 1 B 3 GLU A 36 ILE A 44 0 SHEET 2 B 3 GLY A 70 THR A 80 -1 O ILE A 76 N ILE A 38 SHEET 3 B 3 VAL A 89 ASP A 91 -1 O LEU A 90 N TYR A 75 SHEET 1 C 3 LYS A 51 GLU A 52 0 SHEET 2 C 3 VAL A 102 VAL A 105 1 O VAL A 105 N LYS A 51 SHEET 3 C 3 ILE A 63 THR A 65 -1 N THR A 65 O VAL A 102 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1