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- PDB-1h8g: C-terminal domain of the major autolysin (C-LytA) from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 1h8g
TitleC-terminal domain of the major autolysin (C-LytA) from Streptococcus pneumoniae
ComponentsMAJOR AUTOLYSIN
KeywordsCHOLINE-BINDING DOMAIN / CELL WALL ATTACHMENT
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Cholin Binding / left handed beta-beta-3-solenoid / Ami_2 / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
CHOLINE ION / Autolysin
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsFernandez-Tornero, C. / Garcia, E. / Lopez, R. / Gimenez-Gallego, G. / Romero, A.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factor Lyta
Authors: Fernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A.
#1: Journal: Gene / Year: 1990
Title: Cloning and Expression of Gene Fragments Encoding the Choline-Binding Domain of Pneumococcal Murein Hydrolases
Authors: Sanchez-Puelles, J.M. / Sanz, J.M. / Garcia, J.L. / Garcia, E.
History
DepositionFeb 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR AUTOLYSIN
B: MAJOR AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9338
Polymers22,3082
Non-polymers6256
Water1,09961
1
A: MAJOR AUTOLYSIN
B: MAJOR AUTOLYSIN
hetero molecules

A: MAJOR AUTOLYSIN
B: MAJOR AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,86516
Polymers44,6154
Non-polymers1,25012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)97.571, 97.571, 68.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.75571, -0.19738, -0.62446), (-0.25203, -0.79241, 0.55548), (-0.60447, 0.57717, 0.54908)
Vector: 154.1736, 119.12921, 17.23518)
DetailsTHE CHOLINE-BINDING DOMAIN FRAGMENT CRYSTALLISES AS ATETRAMERIC ASSEMBLY FORMING A CYCLIC DOUGHNUT STRUCTURE.

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Components

#1: Protein MAJOR AUTOLYSIN / C-LYTA / CELL WALL BINDING DOMAIN


Mass: 11153.843 Da / Num. of mol.: 2 / Fragment: CHOLINE-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Cellular location: EXTRACELLULAR / Gene: LYTA / Plasmid: PCE17 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase
#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Description: A FIRST STRUCTURE, WHOSE STATISTICS HAVE NOT BEEN SUBMITTED, WAS DETERMINED TO 3.0 ANGSTROM RESOLUTION THROUGH A MAD EXPERIMENT. A SECOND EXPERIMENT WAS THEN PERFORMED ON A SINGLE ...Description: A FIRST STRUCTURE, WHOSE STATISTICS HAVE NOT BEEN SUBMITTED, WAS DETERMINED TO 3.0 ANGSTROM RESOLUTION THROUGH A MAD EXPERIMENT. A SECOND EXPERIMENT WAS THEN PERFORMED ON A SINGLE CRYSTAL. IT IS STRUCTURE REFINED AGAINST THE DATA FROM THIS SECOND EXPERIMENT THAT IS PRESENTED IN THIS ENTRY
Crystal growpH: 4.6
Details: 30% MPD, 0.2 M NACL, 0.1 M NA-ACETATE, PH 4.6, 0.2 M GUANIDINE-HCL, 0.15 M CHOLINE-CL.
Crystal grow
*PLUS
Temperature: 295 K / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 mg/mlprotein1drop
250 mMTris-HCl1droppH6.5
3100 mM1dropNaCl
4150 mMcholine chloride1drop
530 %(v/v)MPD1reservoir
60.2 M1reservoirNaCl
70.1 Msodium acetate1reservoirpH4.6
80.2 Mguanidine-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9073
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: MIRRORS
RadiationMonochromator: GE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9073 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 12997 / % possible obs: 97.8 % / Observed criterion σ(I): 8 / Redundancy: 3 % / Biso Wilson estimate: 46.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.368 / % possible all: 97.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 13018 / Num. measured all: 117161 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.368

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→32.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1544106.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SEVERAL CYCLES WITH CNS, ONE SHELX CYCLE TO FIND WATER MOLECULES, FINAL CYCLE WITH CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1046 8 %RANDOM
Rwork0.219 ---
obs0.219 12994 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6129 Å2 / ksol: 0.344715 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.01 Å20 Å20 Å2
2--7.01 Å20 Å2
3----14.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 42 61 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 168 7.9 %
Rwork0.317 1953 -
obs--97 %
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Lowest resolution: 2.53 Å

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