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- PDB-1rv9: Crystal Structure of Neisseria meningitidis protein NMB0706, Pfam... -

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Basic information

Entry
Database: PDB / ID: 1rv9
TitleCrystal Structure of Neisseria meningitidis protein NMB0706, Pfam DUF152
Componentsconserved hypothetical protein NMB0706
KeywordsUNKNOWN FUNCTION / alpha-beta-beta-alpha structure / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


2'-deoxyadenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / adenosine deaminase activity / copper ion binding
Similarity search - Function
CNF1/YfiH-like putative cysteine hydrolases / CNF1/YfiH-like putative cysteine hydrolases / Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.53 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a hypothetical protein, NMB0706
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionDec 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein NMB0706
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2502
Polymers27,1541
Non-polymers961
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.850, 41.340, 72.140
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

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Components

#1: Protein conserved hypothetical protein NMB0706


Mass: 27153.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 15676604, UniProt: Q9K0A8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: Ammonium sulfate, HEPES, PEG 400, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 100K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.9792, 0.9795
SYNCHROTRONNSLS X12C20.978
Detector
TypeIDDetectorDate
BRANDEIS - B41CCDAug 10, 2003
Brandeis-B43CCDMay 28, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.9781
ReflectionResolution: 1.53→50 Å / Num. all: 33998 / Num. obs: 33998 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 19.8
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.191 / Num. unique all: 2816 / % possible all: 81.4

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Processing

Software
NameVersionClassification
MARMADdata collection
SCALEPACKdata scaling
SOLVE& SHARPphasing
CNS1refinement
MARMADdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.53→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 1323 -Random
Rwork0.1972 ---
all-31813 --
obs-31813 95.1 %-
Refinement stepCycle: LAST / Resolution: 1.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 5 153 1937
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005427
X-RAY DIFFRACTIONc_angle_deg1.58869

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