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- PDB-1gvm: CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREP... -

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Basic information

Entry
Database: PDB / ID: 1gvm
TitleCHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE
ComponentsAUTOLYSIN
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 / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / Autolysin
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Two New Crystal Forms of the Choline-Binding Domain of the Major Pneumococcal Autolysin: Insights Into the Dynamics of the Active Dimeric
Authors: Fernandez-Tornero, C. / Garcia, E. / Lopez, R. / Gimenez-Gallego, G. / Romero, A.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factorlyta
Authors: Fernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A.
History
DepositionFeb 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AUTOLYSIN
B: AUTOLYSIN
C: AUTOLYSIN
D: AUTOLYSIN
E: AUTOLYSIN
F: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,66728
Polymers95,2606
Non-polymers2,40722
Water1,42379
1
A: AUTOLYSIN
B: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,58710
Polymers31,7532
Non-polymers8338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AUTOLYSIN
D: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4829
Polymers31,7532
Non-polymers7297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: AUTOLYSIN
F: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5989
Polymers31,7532
Non-polymers8447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.717, 85.390, 204.136
Angle α, β, γ (deg.)90.00, 96.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99957, -0.01022, -0.02753), (-0.01794, 0.95479, 0.29676), (0.02325, 0.29712, -0.95456)29.17724, -1.03858, 6.48181
2given(0.35487, 0.88639, -0.2973), (0.88348, -0.42196, -0.20349), (-0.30582, -0.19044, -0.93285)21.75259, -10.66553, 67.84927
3given(-0.41713, 0.77704, 0.47139), (-0.87492, -0.48371, 0.02314), (0.24599, -0.40277, 0.88162)29.90285, 14.57103, 52.50802
4given(-0.50289, 0.86387, 0.02885), (-0.84371, -0.49786, 0.20075), (0.18778, 0.07661, 0.97922)51.17114, 33.0355, 65.55295
5given(0.30394, 0.93954, 0.15776), (0.92603, -0.25245, -0.28059), (-0.2238, 0.23137, -0.94678)37.76469, 6.25918, 80.43757

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Components

#1: Protein
AUTOLYSIN / MAJOR AUTOLYSIN / N-ACETYLMURAMOYL-L-ALANINE AMIDASE / MUREIN HYDROLASE / MUCOPEPTIDE ...MAJOR AUTOLYSIN / N-ACETYLMURAMOYL-L-ALANINE AMIDASE / MUREIN HYDROLASE / MUCOPEPTIDE AMINOHYDROLASE / CELL WALL HYDROLASE


Mass: 15876.638 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Plasmid: PCE17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase
#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALA D 194, DISORDERED SIDE-CHAIN IN PDB ENTRY. THE FIRST THREE RESIDUES OF EACH CHAIN (GLY185, ...ALA D 194, DISORDERED SIDE-CHAIN IN PDB ENTRY. THE FIRST THREE RESIDUES OF EACH CHAIN (GLY185, GLY186, ILE187) ARE ARTIFACTS FROM THE CLONING PROCEDURE.

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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 %
Crystal growpH: 6.4
Details: 30% PEG 4000, 0.2 M NA-ACETATE, 0.1 M AMMONIUM-ACETATE, PH 6.4, 0.15 M CHOLINE-CL, 0.4 MM DDAO.
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
110 mg/mlprotein1drop
250 mMTris-HCl1droppH6.5
3100 mM1dropNaCl
4150 mMcholine chloride1drop
530 %(w/v)PEG40001reservoir
60.2 Mammonium acetate1reservoir
70.1 Msodium citrate1reservoirpH6.4
80.4 mMDDAO1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→33 Å / Num. obs: 23628 / % possible obs: 98.5 % / Observed criterion σ(I): 8 / Redundancy: 3.2 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7
Reflection
*PLUS
Lowest resolution: 33 Å / Num. measured all: 74838 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HCX

1hcx


Resolution: 2.8→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 740335.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1790 8 %RANDOM
Rwork0.226 ---
obs0.226 22605 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0206 Å2 / ksol: 0.436606 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å21.27 Å2
2--7.59 Å20 Å2
3----6.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 162 79 6651
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 301 8 %
Rwork0.322 3461 -
obs--99 %
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shell
*PLUS
Lowest resolution: 2.95 Å

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