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- PDB-2gkp: Protein of Unknown Function NMB0488 from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 2gkp
TitleProtein of Unknown Function NMB0488 from Neisseria meningitidis
Componentshypothetical protein NMB0488
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC83854 / hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyImmunity protein CdiI, Proteobacteria type / Immunity protein Cdil-like superfamily / CDI immunity protein / NMB0488-like fold / NMB0488-like / 3-Layer(aba) Sandwich / Alpha Beta / BETA-MERCAPTOETHANOL / DUF1436 domain-containing protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsOsipiuk, J. / Volkart, L. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of hypothetical protein NMB0488 from Neisseria meningitidis.
Authors: Osipiuk, J. / Volkart, L. / Bargassa, M. / Joachimiak, A.
History
DepositionApr 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 10, 2021Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / struct_conn ...pdbx_distant_solvent_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_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 1.4Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT ...REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein NMB0488
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4424
Polymers19,2791
Non-polymers1633
Water7,062392
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.102, 79.877, 44.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-653-

HOH

21A-773-

HOH

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Components

#1: Protein hypothetical protein NMB0488


Mass: 19279.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0488 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9K0T5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes buffer, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 8, 2006
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.35→30.4 Å / Num. all: 36110 / Num. obs: 36110 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 36
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.07 / Num. unique all: 800 / % possible all: 41.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
SCALEPACKdata scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→30.4 Å / Cor.coef. Fo:Fc: 0.972 / SU B: 1.602 / SU ML: 0.029 / σ(F): 0 / σ(I): 0 / ESU R: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2108 -RANDOM
Rwork0.1541 ---
all0.1536 36032 --
obs0.1536 36032 92.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.782 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20 Å2
2--2.12 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 9 392 1730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9562067
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7032480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91815267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2991512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021190
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2761
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21014
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4691.5879
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13721440
X-RAY DIFFRACTIONr_scbond_it3.1743659
X-RAY DIFFRACTIONr_scangle_it4.084.5609
X-RAY DIFFRACTIONr_rigid_bond_restr2.07831538
X-RAY DIFFRACTIONr_sphericity_free6.4293393
X-RAY DIFFRACTIONr_sphericity_bonded5.08631454
LS refinement shellResolution: 1.347→1.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 92 -
Rwork0.224 1364 -
obs-1364 48.49 %

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