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- PDB-1nmp: Structural genomics, ybgI protein, unknown function -

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Basic information

Entry
Database: PDB / ID: 1nmp
TitleStructural genomics, ybgI protein, unknown function
ComponentsHypothetical protein ybgIHypothesis
Keywordsstructural genomics / unknown function / ybgI / hypothetical protein / toroidal structure / Structure 2 Function Project / S2F
Function / homology
Function and homology information


cell pole / protein hexamerization / response to ionizing radiation / DNA repair / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / NIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GTP cyclohydrolase 1 type 2 homolog / GTP cyclohydrolase 1 type 2 homolog
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLadner, J.E. / Obmolova, G. / Teplyakov, A. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: BMC Struct.Biol. / Year: 2003
Title: Crystal Structure of Escherichia coli Protein ybgI, a toroidal structure with a dinuclear metal site
Authors: Ladner, J.E. / Obmolova, G. / Teplyakov, A. / Howard, A.J. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L.
History
DepositionJan 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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_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_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600HETEROGEN THE IDENTIFICATION OF THE METAL ION IN THE ACTIVE SITE IS NOT KNOWN. HERE IT IS MODELED AS MG+2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein ybgI
B: Hypothetical protein ybgI
C: Hypothetical protein ybgI
D: Hypothetical protein ybgI
E: Hypothetical protein ybgI
F: Hypothetical protein ybgI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,78417
Polymers161,5166
Non-polymers26711
Water10,377576
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hypothetical protein ybgI
F: Hypothetical protein ybgI
hetero molecules

E: Hypothetical protein ybgI
F: Hypothetical protein ybgI
hetero molecules

E: Hypothetical protein ybgI
F: Hypothetical protein ybgI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,80818
Polymers161,5166
Non-polymers29212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14010 Å2
ΔGint-185 kcal/mol
Surface area55870 Å2
MethodPISA, PQS
3
A: Hypothetical protein ybgI
B: Hypothetical protein ybgI
hetero molecules

A: Hypothetical protein ybgI
B: Hypothetical protein ybgI
hetero molecules

A: Hypothetical protein ybgI
B: Hypothetical protein ybgI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,73515
Polymers161,5166
Non-polymers2199
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
4
C: Hypothetical protein ybgI
D: Hypothetical protein ybgI
hetero molecules

C: Hypothetical protein ybgI
D: Hypothetical protein ybgI
hetero molecules

C: Hypothetical protein ybgI
D: Hypothetical protein ybgI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,80818
Polymers161,5166
Non-polymers29212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)156.730, 156.730, 57.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
DetailsThe biological assembly is a hexamer generated by the application of the symmetry operations: -y, x-y, Z and y-x, -x, z. If applied to the entire asymmetric unit, these operations will generate 3 toroids (3 biological assemblies). If applied to any of the dimers, AB, CD or EF, these operations will produce one biological assembly.

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Components

#1: Protein
Hypothetical protein ybgI / Hypothesis


Mass: 26919.400 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Escherichia coli O157:H7
Genus: Escherichia, Escherichia / Species: , Escherichia coli / Strain: , O157:H7 / Gene: YBGI OR B0710 OR Z0861 OR ECS0735 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P75743, UniProt: P0AFP6*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.44 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M cacodylate buffer pH 7.5, 0.1M magnesium acetate, 15% (w/v) polyethylene glycol 8000, 5% (v/v) polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Mcacodylate1reservoirpH7.5
20.1 Mmagnesium acetate1reservoir
315 %(w/v)PEG80001reservoir
45 %(v/v)PEG4001reservoir
54.7 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 80094 / Redundancy: 5 % / Biso Wilson estimate: 4.1 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.1
Reflection
*PLUS
% possible obs: 99.8 % / Num. measured all: 303926
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
MAR345data collection
d*TREKdata reduction
CNSrefinement
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet structure

Resolution: 2.2→19.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 199707.79 / Data cutoff high rms absF: 199707.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4000 5 %RANDOM
Rwork0.212 ---
obs0.212 80007 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.9411 Å2 / ksol: 0.352375 e/Å3
Displacement parametersBiso mean: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å22.53 Å20 Å2
2--2.19 Å20 Å2
3----4.39 Å2
Refine analyzeLuzzati coordinate error free: 0.32 Å / Luzzati sigma a free: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11382 0 11 576 11969
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.582.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
Rfactor% reflection
Rfree0.274 5.1 %
Rwork0.242 -
obs-91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4

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