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- PDB-3slu: Crystal structure of NMB0315 -

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Basic information

Entry
Database: PDB / ID: 3slu
TitleCrystal structure of NMB0315
ComponentsM23 peptidase domain protein
KeywordsHYDROLASE / outer membrane
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #350 / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Peptidase, M23 family
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsShen, Y. / Wang, X. / Yang, X. / Xu, H.
CitationJournal: Plos One / Year: 2011
Title: Crystal structure of outer membrane protein NMB0315 from Neisseria meningitidis.
Authors: Wang, X. / Yang, X. / Yang, C. / Wu, Z. / Xu, H. / Shen, Y.
History
DepositionJun 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: M23 peptidase domain protein
B: M23 peptidase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7764
Polymers79,6592
Non-polymers1172
Water1,36976
1
A: M23 peptidase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8882
Polymers39,8301
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: M23 peptidase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8882
Polymers39,8301
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)195.68, 75.50, 81.64
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein M23 peptidase domain protein / outer membrane protein NMB0315


Mass: 39829.512 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 54-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: ATCC 13091 / Gene: HMPREF0602_0018 / Production host: Escherichia coli (E. coli) / References: UniProt: E0N688
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 7% PEG 20000, 0.1M Tris-HCl, 2% 1,4-Dioxane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9794
SYNCHROTRONSSRF BL17U20.9794
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMay 22, 2010
MARMOSAIC 225 mm CCD2CCDNov 13, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 38289 / Num. obs: 38278 / % possible obs: 82.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Biso Wilson estimate: 40.8 Å2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 50.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→37.75 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2335835.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1916 5 %RANDOM
Rwork0.255 ---
obs0.255 31954 82.7 %-
all-38289 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0085 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 84.8 Å2
Baniso -1Baniso -2Baniso -3
1--19.9 Å20 Å24.83 Å2
2--47.2 Å20 Å2
3----27.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 2.41→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5364 0 2 76 5442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.382.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 198 5.1 %
Rwork0.432 3648 -
obs--49.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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