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- PDB-2fiy: The crystal structure of the FdhE protein from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 2fiy
TitleThe crystal structure of the FdhE protein from Pseudomonas aeruginosa
ComponentsProtein fdhE homolog
KeywordsStructural genomics / unknown function / FdhE protein / Pseudomonas aeruginosa / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein maturation / ferric iron binding / cytosol
Similarity search - Function
FdhE-like fold / FdhE-like domain / Formate dehydrogenase accessory protein / FdhE-like superfamily / Protein involved in formate dehydrogenase formation / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Protein FdhE homolog
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the FdhE protein from Pseudomonas aeruginosa PAO1
Authors: Zhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: 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 / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Protein fdhE homolog
B: Protein fdhE homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0837
Polymers67,8042
Non-polymers2795
Water6,648369
1
A: Protein fdhE homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0143
Polymers33,9021
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fdhE homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0694
Polymers33,9021
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.261, 96.617, 140.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Protein fdhE homolog


Mass: 33901.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: fdhE GI:9951077 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HV00
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.05M (NH4)2SO4, 0.1M Tris pH8.5, 25% P 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→97 Å / Num. all: 35740 / Num. obs: 35601 / % possible obs: 99.61 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 33.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2714 / % possible all: 96.72

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→96.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.745 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.225 / ESU R Free: 0.189
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24264 1890 5 %RANDOM
Rwork0.19665 ---
obs0.19902 35601 99.61 %-
all-35740 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.038 Å0.032 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.031 Å
Refinement stepCycle: LAST / Resolution: 2.1→96.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 5 369 4738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214470
X-RAY DIFFRACTIONr_bond_other_d0.0010.024170
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9886072
X-RAY DIFFRACTIONr_angle_other_deg0.8839643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56122.667195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75815710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2191542
X-RAY DIFFRACTIONr_chiral_restr0.0830.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02905
X-RAY DIFFRACTIONr_nbd_refined0.20.21025
X-RAY DIFFRACTIONr_nbd_other0.1890.24176
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22073
X-RAY DIFFRACTIONr_nbtor_other0.0860.22634
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2306
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.227
X-RAY DIFFRACTIONr_mcbond_it0.9311.53620
X-RAY DIFFRACTIONr_mcbond_other0.1251.51135
X-RAY DIFFRACTIONr_mcangle_it1.05124452
X-RAY DIFFRACTIONr_scbond_it1.46731912
X-RAY DIFFRACTIONr_scangle_it2.1284.51620
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 128 -
Rwork0.208 2497 -
obs--96.72 %
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)
11.5549-0.0422-0.14172.49710.16551.72310.09610.05380.1357-0.015-0.0233-0.228-0.2212-0.0217-0.07280.06240.01520.0489-0.12970.0306-0.119311.20596.42651.631
22.30790.4225-0.23933.10530.41542.8972-0.03530.0295-0.23510.17030.0320.1140.06570.06810.00330.07850.0408-0.0357-0.18080.0047-0.191315.67247.48652.93
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 78
2X-RAY DIFFRACTION1A79 - 180
3X-RAY DIFFRACTION1A181 - 250
4X-RAY DIFFRACTION1A251 - 307
5X-RAY DIFFRACTION2B18 - 78
6X-RAY DIFFRACTION2B79 - 182
7X-RAY DIFFRACTION2B183 - 250
8X-RAY DIFFRACTION2B251 - 308

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