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- PDB-3mw6: Crystal structure of NMB1681 from Neisseria meningitidis MC58, a ... -

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Basic information

Entry
Database: PDB / ID: 3mw6
TitleCrystal structure of NMB1681 from Neisseria meningitidis MC58, a FinO-like RNA chaperone
Componentsuncharacterized protein NMB1681
Keywordsstructural genomics / unknown function / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homologyFertility Inhibition Protein O; Chain: A; Domain 1 / ProQ/FinO domain / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family / Orthogonal Bundle / Mainly Alpha / ProQ domain-containing protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.209 Å
AuthorsTan, K. / Zhou, M. / Duggan, E. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Rna Biol. / Year: 2010
Title: N. meningitidis 1681 is a member of the FinO family of RNA chaperones.
Authors: Chaulk, S. / Lu, J. / Tan, K. / Arthur, D.C. / Edwards, R.A. / Frost, L.S. / Joachimiak, A. / Glover, J.N.
History
DepositionMay 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
SupersessionJul 14, 2010ID: 2HXJ
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein NMB1681
B: uncharacterized protein NMB1681
C: uncharacterized protein NMB1681
D: uncharacterized protein NMB1681
E: uncharacterized protein NMB1681
F: uncharacterized protein NMB1681
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6947
Polymers95,6016
Non-polymers921
Water3,063170
1
A: uncharacterized protein NMB1681
B: uncharacterized protein NMB1681


Theoretical massNumber of molelcules
Total (without water)31,8672
Polymers31,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-8 kcal/mol
Surface area13010 Å2
MethodPISA
2
C: uncharacterized protein NMB1681
D: uncharacterized protein NMB1681
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9593
Polymers31,8672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area12840 Å2
MethodPISA
3
D: uncharacterized protein NMB1681

E: uncharacterized protein NMB1681

F: uncharacterized protein NMB1681


Theoretical massNumber of molelcules
Total (without water)47,8013
Polymers47,8013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area2210 Å2
ΔGint-22 kcal/mol
Surface area20160 Å2
MethodPISA
4
E: uncharacterized protein NMB1681
F: uncharacterized protein NMB1681


Theoretical massNumber of molelcules
Total (without water)31,8672
Polymers31,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.479, 76.527, 122.715
Angle α, β, γ (deg.)90.00, 116.84, 90.00
Int Tables number5
Space group name H-MC121
DetailsExperimentally unknown. Possibly, the chains A and B, C and D, E and F form dimers respectively.

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Components

#1: Protein
uncharacterized protein NMB1681


Mass: 15933.576 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB1681 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JY98
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100MM BIS-TRIS, 170MM MGCL2, 21% PEG3350, pH 6.5, 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: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2001 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.2→109 Å / Num. obs: 96019 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.2
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.92 / Num. unique all: 2736 / % possible all: 79.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.209→42.889 Å / SU ML: 0.33 / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 4882 5.08 %random
Rwork0.1906 ---
all0.1929 96019 --
obs0.1929 96019 93.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.951 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.3771 Å20 Å2-4.0939 Å2
2--15.8526 Å20 Å2
3----7.4755 Å2
Refinement stepCycle: LAST / Resolution: 2.209→42.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5393 0 6 170 5569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085526
X-RAY DIFFRACTIONf_angle_d1.0267435
X-RAY DIFFRACTIONf_dihedral_angle_d18.1772110
X-RAY DIFFRACTIONf_chiral_restr0.069809
X-RAY DIFFRACTIONf_plane_restr0.005976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2086-2.28760.31253030.27765793X-RAY DIFFRACTION59
2.2876-2.37910.31984410.24918370X-RAY DIFFRACTION85
2.3791-2.48740.28544860.23389326X-RAY DIFFRACTION96
2.4874-2.61850.29045430.22399681X-RAY DIFFRACTION99
2.6185-2.78260.27495200.21059664X-RAY DIFFRACTION99
2.7826-2.99740.28235160.22079683X-RAY DIFFRACTION99
2.9974-3.29890.25525150.21039716X-RAY DIFFRACTION99
3.2989-3.7760.20735470.17769689X-RAY DIFFRACTION99
3.776-4.75640.20585570.14519635X-RAY DIFFRACTION99
4.7564-42.89710.18484540.16679580X-RAY DIFFRACTION97
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)
11.2157-0.3438-0.29421.75111.50931.93320.0589-0.1024-0.0623-0.03090.0376-0.21560.01190.0772-0.09050.24090.0597-0.02650.2045-0.05860.2175-14.96161.224-25.3654
20.92380.8498-0.66821.031-0.31181.392-0.2505-0.2152-0.49770.02780.021-0.3614-0.01850.33280.17230.19960.14360.09620.50450.14380.4563-23.9174-21.0125-42.1572
31.0587-0.44760.63581.1588-0.83521.80040.07880.3364-0.0865-0.153-0.14020.053-0.0417-0.03890.06620.27990.06040.0210.5460.02460.2332-48.7744-6.8645-45.2942
41.6557-0.32280.5341.5972-0.91252.1707-0.0138-0.1026-0.03090.0758-0.01560.02790.15190.26620.05740.29310.03640.03910.29480.09650.2217-46.1678-11.4627-12.3633
51.3321.37890.45232.01160.38021.19970.1586-0.21270.29220.0441-0.25630.33870.0334-0.23620.0790.2302-0.0067-00.23-0.02430.3438-74.8053-0.0063-17.2656
62.5332-0.84461.10690.25540.61531.10020.0210.10540.3673-0.0111-0.0927-0.0261-0.090.09970.05210.31820.0004-0.03770.21660.04580.341-51.275921.7346-22.8186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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