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- PDB-4o2h: Crystal structure of BCAM1869 protein (RsaM homolog) from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 4o2h
TitleCrystal structure of BCAM1869 protein (RsaM homolog) from Burkholderia cenocepacia
Componentsprotein BCAM1869
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / quorum sensing
Function / homologyNuclear Transport Factor 2; Chain: A, - #610 / Transcriptional regulator RsaM-like / Domain of unknown function (DUF4902) / Nuclear Transport Factor 2; Chain: A, / Roll / identical protein binding / Alpha Beta / DUF4902 domain-containing protein
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsMichalska, K. / Chhor, G. / Clancy, S. / Winans, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Febs J. / Year: 2014
Title: RsaM: a transcriptional regulator of Burkholderia spp. with novel fold.
Authors: Michalska, K. / Chhor, G. / Clancy, S. / Jedrzejczak, R. / Babnigg, G. / Winans, S.C. / Joachimiak, A.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 20, 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_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein BCAM1869
B: protein BCAM1869


Theoretical massNumber of molelcules
Total (without water)31,3362
Polymers31,3362
Non-polymers00
Water55831
1
A: protein BCAM1869

A: protein BCAM1869


Theoretical massNumber of molelcules
Total (without water)31,3362
Polymers31,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area13770 Å2
MethodPISA
2
B: protein BCAM1869

B: protein BCAM1869


Theoretical massNumber of molelcules
Total (without water)31,3362
Polymers31,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area1820 Å2
ΔGint-11 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.146, 69.146, 216.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

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Components

#1: Protein protein BCAM1869


Mass: 15668.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BCAM1869 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: B4EMD1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ca acetate, 10% PEG8K, 0.1 M HEPES:NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 14514 / Num. obs: 14488 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 59.66 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 47
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.924 / Mean I/σ(I) obs: 2.8 / Num. unique all: 688 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHARPphasing
PHASERphasing
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→20.2 Å / Cor.coef. Fo:Fc: 0.9476 / Cor.coef. Fo:Fc free: 0.9204 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT RIDING POSITIONS. THE STRUCTURE WAS SOLVED BY MIRAS ON A DIFFERENT CRYSTAL FORM AND TWO DERIVATIVES AND FOLLOWED BY MR WITH A PARTIAL MODEL ON THE CURRENT DATASET.
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 725 5.03 %RANDOM
Rwork0.2147 ---
all0.2166 14413 --
obs0.2166 14413 --
Displacement parametersBiso mean: 65.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.597 Å20 Å20 Å2
2--2.597 Å20 Å2
3----5.1939 Å2
Refine analyzeLuzzati coordinate error obs: 0.469 Å
Refinement stepCycle: LAST / Resolution: 2.3→20.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 0 31 1998
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112012HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.072759HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d871SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes308HARMONIC5
X-RAY DIFFRACTIONt_it2012HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion2.52
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2249SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.48 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2972 140 4.86 %
Rwork0.2408 2740 -
all0.2435 2880 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.42441.0238-0.24042.93581.42270.44970.1746-0.5299-0.38530.2295-0.0321-0.37430.354-0.3212-0.1425-0.0202-0.1413-0.0592-0.04220.0932-0.15117.7044-15.2761-5.3654
24.1088-0.12963.22.8125-0.86070.22090.00840.0854-0.0149-0.0891-0.0702-0.1015-0.3379-0.42020.06170.2292-0.02320.044-0.09360.0238-0.142616.14887.2845-19.4797
33.03212.69041.86982.14820.72552.44830.3084-0.3744-0.4885-0.0649-0.0368-0.24230.0852-0.2759-0.2716-0.0194-0.0979-0.009-0.11450.0572-0.042819.9954-10.8429-9.3978
42.7659-0.40582.23412.93131.95134.77540.0962-0.38670.41910.1389-0.23660.0843-0.208-0.69690.1404-0.0877-0.01730.00420.0081-0.0504-0.125114.092-3.318-5.0481
50.7-0.5293-1.13930.38631.2090.9583-0.0116-0.00260.0646-0.00260.04520.0899-0.077-0.0853-0.03360.1812-0.15620.06920.03910.017-0.11919.7225-5.8193-0.5572
60.4946-0.49011.20470.9359-1.81660.3867-0.0711-0.10380.00310.08550.1078-0.4453-0.0476-0.0098-0.03670.0689-0.11290.0117-0.12570.01490.007825.6358-3.0091-7.3703
7-0.10050.058-0.53630.10050.706700.01630.0264-0.0191-0.0382-0.0146-0.02550.0045-0.0024-0.00170.0232-0.13780.1256-0.1558-0.0040.130131.5649-3.5856-22.8834
80.48580.11761.00172.2823-2.78232.0949-0.0141-0.2649-0.1130.3224-0.0304-0.11410.0855-0.10820.0445-0.0064-0.2853-0.0692-0.02790.13550.046613.5207-34.7650.8215
91.29980.0122-0.0268-0.4192-0.74283.7946-0.0451-0.0466-0.41920.11140.0395-0.22160.05140.38980.0056-0.1772-0.11740.1299-0.27750.07890.2729.9249-57.69-16.7893
100.23482.71081.21873.16642.79612.3397-0.052-0.1422-0.46590.2673-0.1004-0.1997-0.23810.23110.1524-0.0755-0.2060.0267-0.18860.19090.28868.5414-46.8401-9.9315
112.892-2.68081.06621.8152-2.08732.2876-0.03160.0051-0.00330.04760.012-0.08740.05440.06640.01970.0921-0.06290.0368-0.18630.18840.28079.2002-61.6384-11.0339
12-2.37581.30271.45972.6148-0.40300.0123-0.0783-0.02860.0769-0.0190.0149-0.00120.03130.0067-0.0466-0.1437-0.063-0.23170.13910.183617.6268-43.585-3.6068
13-0.2472-0.86271.89144.4026-1.65570.0695-0.0550.0203-0.0360.0822-0.01710.01840.12430.00790.0720.0324-0.0506-0.043-0.26020.15070.284816.7139-50.2487-0.0582
141.45850.06441.15026.6483-1.33890.01360.07320.0275-0.08830.004-0.12-0.0504-0.0265-0.06260.0468-0.0606-0.19620.1445-0.18510.05360.1283-0.5152-53.4144-15.2811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - A|43}A2 - 43
2X-RAY DIFFRACTION2{A|44 - A|57}A44 - 57
3X-RAY DIFFRACTION3{A|58 - A|79}A58 - 79
4X-RAY DIFFRACTION4{A|80 - A|106}A80 - 106
5X-RAY DIFFRACTION5{A|107 - A|117}A107 - 117
6X-RAY DIFFRACTION6{A|118 - A|132}A118 - 132
7X-RAY DIFFRACTION7{A|133 - A|138}A133 - 138
8X-RAY DIFFRACTION8{B|3 - B|26}B3 - 26
9X-RAY DIFFRACTION9{B|27 - B|56}B27 - 56
10X-RAY DIFFRACTION10{B|57 - B|80}B57 - 80
11X-RAY DIFFRACTION11{B|81 - B|93}B81 - 93
12X-RAY DIFFRACTION12{B|94 - B|100}B94 - 100
13X-RAY DIFFRACTION13{B|105 - B|122}B105 - 122
14X-RAY DIFFRACTION14{B|123 - B|138}B123 - 138

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