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- PDB-3bid: Crystal structure of the NMB1088 protein from Neisseria meningiti... -

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Basic information

Entry
Database: PDB / ID: 3bid
TitleCrystal structure of the NMB1088 protein from Neisseria meningitidis. Northeast Structural Genomics Consortium target MR91
ComponentsUPF0339 protein NMB1088
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYegP-like / Domain of unknown function DUF1508 / Domain of unknown function (DUF1508) / YegP-like superfamily / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / UPF0339 protein NMB1088
Function and homology information
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Fang, Y. / Xiao, R. / Owen, L.A. / Maglaqui, M. / Cunningham, K. / Baran, M.C. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Fang, Y. / Xiao, R. / Owen, L.A. / Maglaqui, M. / Cunningham, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the NMB1088 protein from Neisseria meningitidis.
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Fang, Y. / Xiao, R. / Owen, L.A. / Maglaqui, M. / Cunningham, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 22, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _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: UPF0339 protein NMB1088
B: UPF0339 protein NMB1088
C: UPF0339 protein NMB1088
D: UPF0339 protein NMB1088
E: UPF0339 protein NMB1088
F: UPF0339 protein NMB1088
G: UPF0339 protein NMB1088
H: UPF0339 protein NMB1088


Theoretical massNumber of molelcules
Total (without water)60,2508
Polymers60,2508
Non-polymers00
Water50428
1
A: UPF0339 protein NMB1088
B: UPF0339 protein NMB1088


Theoretical massNumber of molelcules
Total (without water)15,0632
Polymers15,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-19 kcal/mol
Surface area6810 Å2
MethodPISA
2
C: UPF0339 protein NMB1088
D: UPF0339 protein NMB1088


Theoretical massNumber of molelcules
Total (without water)15,0632
Polymers15,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-19 kcal/mol
Surface area6790 Å2
MethodPISA
3
E: UPF0339 protein NMB1088
F: UPF0339 protein NMB1088


Theoretical massNumber of molelcules
Total (without water)15,0632
Polymers15,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-21 kcal/mol
Surface area7500 Å2
MethodPISA
4
G: UPF0339 protein NMB1088
H: UPF0339 protein NMB1088


Theoretical massNumber of molelcules
Total (without water)15,0632
Polymers15,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-19 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.743, 60.040, 64.370
Angle α, β, γ (deg.)89.39, 90.81, 103.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
UPF0339 protein NMB1088


Mass: 7531.301 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Species: Neisseria meningitidis / Strain: MC58 / Serogroup B / Gene: NMB1088, 903505 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7DDI1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM Na3 Citrate pH 4.0, 40% PEG 1000, 100 mM (NH4)H2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 30, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 27651 / Num. obs: 27651 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.07 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.41 / Num. unique all: 2571 / Rsym value: 0.224 / % possible all: 87.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.81 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 681025.46 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2064 9.2 %RANDOM
Rwork0.241 ---
all0.244 27649 --
obs0.241 22534 81.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9404 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.53 Å2-6.81 Å22.84 Å2
2--23.64 Å25.54 Å2
3----13.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 0 28 3787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.427 150 9.7 %
Rwork0.336 1399 -
obs-1399 56.9 %

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