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- PDB-2o1e: Crystal Structure of the Metal-dependent Lipoprotein YcdH from Ba... -

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Basic information

Entry
Database: PDB / ID: 2o1e
TitleCrystal Structure of the Metal-dependent Lipoprotein YcdH from Bacillus subtilis, Northeast Structural Genomics Target SR583
ComponentsYcdH
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


zinc ion transport / cell adhesion / metal ion binding / plasma membrane
Similarity search - Function
Adhesin B / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / High-affinity zinc uptake system binding-protein ZnuA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsForouhar, F. / Zhou, W. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M.C. ...Forouhar, F. / Zhou, W. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Metal-dependent Lipoprotein YcdH from Bacillus subtilis, Northeast Structural Genomics Target SR583
Authors: Forouhar, F. / Zhou, W. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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: YcdH
B: YcdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0214
Polymers70,9112
Non-polymers1102
Water63135
1
A: YcdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5102
Polymers35,4551
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YcdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5102
Polymers35,4551
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.292, 54.344, 62.840
Angle α, β, γ (deg.)103.70, 100.46, 96.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein YcdH


Mass: 35455.391 Da / Num. of mol.: 2 / Fragment: residues 22-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ycdH, locus_tag=BSU02850 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O34966
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Tris-HCl, 40% PEG1k, 100 mM magnesium acetate, and 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→39.7 Å / Num. all: 37295 / Num. obs: 35170 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.05 / Net I/σ(I): 11.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 2.22 / Rsym value: 0.248 / % possible all: 88.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 162118.17 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2696 9.6 %RANDOM
Rwork0.223 ---
obs0.223 28076 81 %-
all-34661 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.31 Å2 / ksol: 0.315655 e/Å3
Displacement parametersBiso mean: 61.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.41 Å210.17 Å28.7 Å2
2---2.52 Å213.64 Å2
3----5.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 0 2 35 4236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 303 10.1 %
Rwork0.345 2711 -
obs--52.5 %

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