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- PDB-3s99: Crystal structure of a basic membrane lipoprotein from brucella m... -

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Basic information

Entry
Database: PDB / ID: 3s99
TitleCrystal structure of a basic membrane lipoprotein from brucella melitensis, iodide soak
ComponentsBasic membrane lipoprotein
KeywordsLIPID BINDING PROTEIN / SSGCID / Basic membrane lipoprotein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Adenine
Function / homology
Function and homology information


ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / IODIDE ION / Purine-binding protein BAB2_0673
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a basic membrane lipoprotein from brucella melitensis, iodide soak
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Edwards, T.E. / Staker, B.L.
History
DepositionJun 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic membrane lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,65820
Polymers39,3411
Non-polymers2,31719
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.640, 85.850, 95.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Basic membrane lipoprotein


Mass: 39341.492 Da / Num. of mol.: 1 / Fragment: unp residues 17-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: ABORTUS 2308 / Gene: BAB2_0673 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YKI6
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 100MM BISTRIS, 200MM NACL; BRABA.17960.A.A2, PS01053 AT 37.0MG/ML, CRYSTALS SOAKED FOR 30MIN IN 25% PEG 3350, 100M BISTRIS, 200MM NACL, 10% EG, 300MM NAI, VAPOR DIFFUSION, ...Details: 25% PEG 3350, 100MM BISTRIS, 200MM NACL; BRABA.17960.A.A2, PS01053 AT 37.0MG/ML, CRYSTALS SOAKED FOR 30MIN IN 25% PEG 3350, 100M BISTRIS, 200MM NACL, 10% EG, 300MM NAI, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 23, 2011
RadiationMonochromator: Rigaku VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 21344 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 28.18 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 24.32
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1581 / Rsym value: 0.297 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD
Starting model: solved via SAD phasing based on iodide ions

Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.746 / SU ML: 0.1 / Isotropic thermal model: isotropic TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1093 5.1 %RANDOM
Rwork0.177 ---
all0.179 21867 --
obs0.179 20305 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--2.29 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 28 250 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222597
X-RAY DIFFRACTIONr_bond_other_d0.0010.021709
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9443528
X-RAY DIFFRACTIONr_angle_other_deg0.88834174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72425.043115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.183159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6621.51634
X-RAY DIFFRACTIONr_mcbond_other0.1771.5674
X-RAY DIFFRACTIONr_mcangle_it1.16822610
X-RAY DIFFRACTIONr_scbond_it1.9723963
X-RAY DIFFRACTIONr_scangle_it2.9854.5918
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 60 -
Rwork0.205 1328 -
obs--88.07 %
Refinement TLS params.Method: refined / Origin x: 37.57 Å / Origin y: 23.293 Å / Origin z: 41.66 Å
111213212223313233
T0.023 Å2-0.0072 Å20.0105 Å2-0.038 Å20.0014 Å2--0.0076 Å2
L1.431 °2-0.3404 °20.8191 °2-0.3027 °2-0.408 °2--1.4945 °2
S-0.0061 Å °-0.1093 Å °-0.016 Å °0.0029 Å °0.003 Å °-0.0168 Å °0.0289 Å °-0.0955 Å °0.0031 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 349
2X-RAY DIFFRACTION1A351 - 400
3X-RAY DIFFRACTION1A402 - 651

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