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- PDB-3cx3: Crystal structure Analysis of the Streptococcus pneumoniae AdcAII... -

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Basic information

Entry
Database: PDB / ID: 3cx3
TitleCrystal structure Analysis of the Streptococcus pneumoniae AdcAII protein
ComponentsLipoprotein
KeywordsMETAL BINDING PROTEIN / zinc-binding / Lipoprotein / Transport / LIPID BINDING PROTEIN
Function / homology
Function and homology information


zinc ion transport / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsLoisel, E. / Durmort, C. / Jacquamet, L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: AdcAII, a new pneumococcal Zn-binding protein homologous with ABC transporters: biochemical and structural analysis.
Authors: Loisel, E. / Jacquamet, L. / Serre, L. / Bauvois, C. / Ferrer, J.L. / Vernet, T. / Di Guilmi, A.M. / Durmort, C.
History
DepositionApr 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Lipoprotein
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9556
Polymers63,7782
Non-polymers1774
Water2,594144
1
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0004
Polymers31,8891
Non-polymers1113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9542
Polymers31,8891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.760, 63.260, 151.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipoprotein / AdcAII / Adhesion lipoprotein


Mass: 31888.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: signal-peptide not encoded / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: lmb, spr0906 / Plasmid: pLIM01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DQ09
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 2000, NaCl, citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.971968, 0.979648, 0.979896
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9719681
20.9796481
30.9798961
ReflectionResolution: 2.4→44.9 Å / Num. all: 40540 / Num. obs: 38743 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.071 / Net I/σ(I): 12.91
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3981 / Rsym value: 0.52 / % possible all: 66.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementResolution: 2.4→44.9 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1064 5 %RANDOM
Rwork0.225 ---
obs0.229 21262 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.198 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å20 Å20 Å2
2---3.72 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 4 144 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224219
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9685702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0375526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00426.066183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.16715777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.113158
X-RAY DIFFRACTIONr_chiral_restr0.1720.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023122
X-RAY DIFFRACTIONr_nbd_refined0.2830.22321
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22826
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2206
X-RAY DIFFRACTIONr_metal_ion_refined0.1760.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.26
X-RAY DIFFRACTIONr_mcbond_it1.6021.52633
X-RAY DIFFRACTIONr_mcangle_it2.84124261
X-RAY DIFFRACTIONr_scbond_it2.48131586
X-RAY DIFFRACTIONr_scangle_it4.1434.51440
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 69 -
Rwork0.279 1307 -
all-1376 -
obs--100 %

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