HEADER HYDROLASE 08-APR-16 5J8T TITLE NMR STRUCTURE OF EXCALIBUR DOMAIN OF CBPL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHOLINE BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.96; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FIRST THREE RESIDUES GAS CORRESPOND TO THE TAG COMPND 7 USED IN THE PRODUCTION . THE FIRST RESIDUE OF THE PROTEIN IS THE COMPND 8 FIRST E IN THE SEQUENCE WITH THE NUMBER 24 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: LYTB_2, ERS020147_00413; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PETTEV28 KEYWDS EXCALIBUR, CHOLINE-BINDING PROTEIN L, PNEUMOCOCCAL ADHESION, KEYWDS 2 HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.PANTOJA-UCEDA,M.A.TREVINO,M.BRUIX REVDAT 4 23-OCT-19 5J8T 1 REMARK SITE REVDAT 3 08-MAY-19 5J8T 1 REMARK REVDAT 2 06-SEP-17 5J8T 1 ATOM REVDAT 1 10-MAY-17 5J8T 0 JRNL AUTH J.GUTIERREZ-FERNANDEZ,M.ALCORLO,S.GALAN-BARTUAL, JRNL AUTH 2 D.PANTOJA-UCEDA,M.A.TREVINO,M.BRUIX,S.HAMMERSCHMIDT, JRNL AUTH 3 J.A.HERMOSO JRNL TITL MOLECULAR CHOLINE-BINDIND PROTEIN L INVOLVED IN PNEUMOCOCCAL JRNL TITL 2 ADHESION AND VIRULENCE THROUGH EXPOSED EXCALIBUR DOMANIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE 20 CONFORMERS WITH THE LOWEST REMARK 3 TARGER FUNCIOTN VALUES FO CYANA CALCULATION WERE SELECTED FOR REMARK 3 FURTHER REFINEMENT AND MINIMIZED WITH AMBER 9.0 USING GIBBS- REMARK 3 BOLTZMAN CONTINUUM SOLVATION MODEL REMARK 4 REMARK 4 5J8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000218219. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.15 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : UNKNOWN REMARK 210 PRESSURE : UNKNOWN ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 EXCALIBUR DOMAIN OF CBPL, 3 MM REMARK 210 CACL2, 1 % DSS, 90% H2O/10% D2O; REMARK 210 0.5 MM EXCALIBUR DOMAIN OF CBPL, REMARK 210 3 MM CACL2, 1 % DSS, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D HNCO; 3D HNCOI; 3D HNCA; 3D REMARK 210 HNCAI; 3D HNCACB; 3D CBCA(CO)NH; REMARK 210 3D H(CCCO)NH; 3D (H)CC(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D H(NCOCA)NH; 3D (H) REMARK 210 N(COCA)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, NMRPIPE 3.0, SPARKY REMARK 210 3.113, NMRVIEW 5.0.20, CYANA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 80 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 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 4 GLU A 67 OE1 - CD - OE2 ANGL. DEV. = -9.1 DEGREES REMARK 500 6 GLU A 67 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 12 GLU A 67 OE1 - CD - OE2 ANGL. DEV. = -8.7 DEGREES REMARK 500 16 GLU A 67 OE1 - CD - OE2 ANGL. DEV. = -7.3 DEGREES REMARK 500 20 GLU A 67 OE1 - CD - OE2 ANGL. DEV. = -7.7 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 61 55.78 30.96 REMARK 500 2 GLU A 28 14.09 -69.38 REMARK 500 2 ASN A 29 35.92 -72.20 REMARK 500 2 HIS A 61 48.36 31.36 REMARK 500 3 HIS A 61 48.76 30.14 REMARK 500 4 GLU A 27 61.49 -118.94 REMARK 500 4 HIS A 61 52.52 29.65 REMARK 500 5 HIS A 61 45.03 31.67 REMARK 500 5 LEU A 68 29.26 -144.47 REMARK 500 6 HIS A 61 49.90 33.43 REMARK 500 6 LEU A 68 -33.52 -133.18 REMARK 500 7 HIS A 61 50.82 30.71 REMARK 500 7 LYS A 69 94.74 -63.77 REMARK 500 8 HIS A 61 50.19 32.08 REMARK 500 9 HIS A 61 42.09 35.11 REMARK 500 10 HIS A 61 52.07 29.78 REMARK 500 11 GLU A 27 40.67 -70.80 REMARK 500 11 HIS A 61 47.19 31.24 REMARK 500 12 HIS A 61 45.70 32.92 REMARK 500 13 GLU A 28 44.44 -72.75 REMARK 500 13 HIS A 61 43.01 32.26 REMARK 500 14 HIS A 61 50.78 31.96 REMARK 500 15 GLU A 28 31.91 -77.82 REMARK 500 15 HIS A 61 50.63 30.09 REMARK 500 16 GLU A 28 102.98 -58.64 REMARK 500 16 HIS A 61 45.92 35.28 REMARK 500 16 LYS A 69 106.79 -59.72 REMARK 500 17 HIS A 61 47.95 33.34 REMARK 500 18 HIS A 61 50.98 30.16 REMARK 500 19 HIS A 61 50.89 31.36 REMARK 500 19 LEU A 68 -21.59 -142.41 REMARK 500 20 HIS A 61 42.74 36.89 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 A 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 58 OD1 REMARK 620 2 ASP A 58 OD2 47.5 REMARK 620 3 ASP A 60 OD1 66.8 70.2 REMARK 620 4 ASP A 60 OD2 75.7 107.0 44.4 REMARK 620 5 ASP A 62 OD1 107.5 152.5 114.3 70.1 REMARK 620 6 ASP A 62 OD2 71.6 108.9 120.2 85.5 44.4 REMARK 620 7 GLU A 67 OE1 134.7 90.0 119.2 142.9 108.6 120.5 REMARK 620 8 GLU A 67 OE2 157.8 133.4 135.2 116.7 64.0 90.4 44.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30064 RELATED DB: BMRB DBREF1 5J8T A 27 70 UNP A0A0U0AG78_STREE DBREF2 5J8T A A0A0U0AG78 27 70 SEQADV 5J8T GLY A 24 UNP A0A0U0AG7 EXPRESSION TAG SEQADV 5J8T ALA A 25 UNP A0A0U0AG7 EXPRESSION TAG SEQADV 5J8T SER A 26 UNP A0A0U0AG7 EXPRESSION TAG SEQRES 1 A 47 GLY ALA SER GLU GLU ASN ILE HIS PHE SER SER CYS LYS SEQRES 2 A 47 GLU ALA TRP ALA ASN GLY TYR SER ASP ILE HIS GLU GLY SEQRES 3 A 47 GLU PRO GLY TYR SER ALA LYS LEU ASP ARG ASP HIS ASP SEQRES 4 A 47 GLY VAL ALA CYS GLU LEU LYS ASN HET CA A 101 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 AA1 SER A 34 ASN A 41 1 8 SSBOND 1 CYS A 35 CYS A 66 1555 1555 2.05 LINK OD1 ASP A 58 CA CA A 101 1555 1555 2.88 LINK OD2 ASP A 58 CA CA A 101 1555 1555 2.31 LINK OD1 ASP A 60 CA CA A 101 1555 1555 3.06 LINK OD2 ASP A 60 CA CA A 101 1555 1555 2.31 LINK OD1 ASP A 62 CA CA A 101 1555 1555 3.07 LINK OD2 ASP A 62 CA CA A 101 1555 1555 2.30 LINK OE1 GLU A 67 CA CA A 101 1555 1555 2.31 LINK OE2 GLU A 67 CA CA A 101 1555 1555 3.02 SITE 1 AC1 5 ASP A 58 ASP A 60 ASP A 62 VAL A 64 SITE 2 AC1 5 GLU A 67 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