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- PDB-3nym: The crystal structure of functionally unknown protein from Neisse... -

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Basic information

Entry
Database: PDB / ID: 3nym
TitleThe crystal structure of functionally unknown protein from Neisseria meningitidis MC58
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #10 / : / Family of unknown function (DUF6853) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / ACETATE ION / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Tan, K. / Volkart, L. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of functionally unknown protein from Neisseria meningitidis MC58
Authors: Zhang, R. / Tan, K. / Volkart, L. / Bargassa, M. / Joachimiak, A.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8108
Polymers30,2412
Non-polymers5706
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-84 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.646, 35.741, 101.565
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. The chains A and B are predicted to form a dimer.

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Components

#1: Protein uncharacterized protein


Mass: 15120.274 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: NMB0500, NMB1774 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JS17
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris, 25% w/v 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→34 Å / Num. all: 24360 / Num. obs: 24360 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 1034 / % possible all: 84.9

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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: 1.9→33.682 Å / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 1178 5.15 %random
Rwork0.1726 ---
all0.1745 22860 --
obs0.1745 22860 91.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.974 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.7972 Å20 Å2-0.518 Å2
2--14.4827 Å20 Å2
3----8.6855 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 35 157 2215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062103
X-RAY DIFFRACTIONf_angle_d0.9222839
X-RAY DIFFRACTIONf_dihedral_angle_d15.401765
X-RAY DIFFRACTIONf_chiral_restr0.068309
X-RAY DIFFRACTIONf_plane_restr0.003351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.98640.34221270.25852156X-RAY DIFFRACTION74
1.9864-2.09110.26071460.21542477X-RAY DIFFRACTION85
2.0911-2.22210.25211380.18262633X-RAY DIFFRACTION90
2.2221-2.39360.23131410.17682733X-RAY DIFFRACTION92
2.3936-2.63440.20911320.17452813X-RAY DIFFRACTION95
2.6344-3.01540.23661550.18262892X-RAY DIFFRACTION97
3.0154-3.79830.21291670.16942939X-RAY DIFFRACTION99
3.7983-33.68770.15281720.14633039X-RAY DIFFRACTION99
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)
10.91520.05020.50110.38850.07710.8870.0318-0.3038-0.03740.04250.004-0.0021-0.0584-0.1199-0.02540.1991-0.00030.02160.28090.00750.190612.43610.749333.524
20.9514-0.00840.56950.1003-0.0530.95560.02720.0241-0.0557-0.04490.00160.0037-0.02360.1168-0.02610.21580.0120.00010.1863-0.00810.202911.89858.587716.0278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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