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- PDB-4lk8: Crystal structure of CyaY protein from Psychromonas ingrahamii in... -

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Basic information

Entry
Database: PDB / ID: 4lk8
TitleCrystal structure of CyaY protein from Psychromonas ingrahamii in complex with Co(II)
ComponentsProtein CyaY
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferric iron binding / ferrous iron binding / cytosol
Similarity search - Function
: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily ...: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Iron-sulfur cluster assembly protein CyaY
Similarity search - Component
Biological speciesPsychromonas ingrahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsNoguera, M.E. / Roman, E.A. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2015
Title: Structural characterization of metal binding to a cold-adapted frataxin
Authors: Noguera, M.E. / Roman, E.A. / Rigal, J.B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionJul 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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Assembly

Deposited unit
A: Protein CyaY
B: Protein CyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9448
Polymers24,5912
Non-polymers3546
Water2,540141
1
A: Protein CyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4724
Polymers12,2951
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein CyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4724
Polymers12,2951
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.891, 50.564, 46.310
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 105 / Label seq-ID: 1 - 105

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Protein CyaY


Mass: 12295.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychromonas ingrahamii (bacteria) / Strain: 37 / Gene: cyaY, Ping_0042 / Plasmid: pJexpress411:56977 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A1SR01
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 20mM sodium acetate, 200mM MgCl2, 29.5% PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91907 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2012
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91907 Å / Relative weight: 1
ReflectionResolution: 1.494→30.425 Å / Num. all: 53634 / Num. obs: 53634 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.61 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.5-1.55177.3
1.55-1.62191
1.62-1.69194.1
1.69-1.78195.3
1.78-1.89195.1
1.89-2.04194.3
2.04-2.24193.3
2.24-2.56196.5
2.56-3.23196.3
3.23-30.43187.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HS5

4hs5


Resolution: 1.494→30.425 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 23.5 / Stereochemistry target values: ML
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED 2. THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS UNDER F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 2689 5.01 %RANDOM
Rwork0.1839 ---
obs0.1853 53620 91.53 %-
all-53634 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.75 Å2 / Biso mean: 27.8952 Å2 / Biso min: 12.05 Å2
Refinement stepCycle: LAST / Resolution: 1.494→30.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 6 141 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191773
X-RAY DIFFRACTIONf_angle_d1.7812398
X-RAY DIFFRACTIONf_dihedral_angle_d13.431645
X-RAY DIFFRACTIONf_chiral_restr0.081254
X-RAY DIFFRACTIONf_plane_restr0.011319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A960X-RAY DIFFRACTION8.355TORSIONAL
12B960X-RAY DIFFRACTION8.355TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4942-1.52140.29681270.26831853198065
1.5214-1.55060.3364950.25532373246881
1.5506-1.58230.3351400.22682604274489
1.5823-1.61670.27721410.22082748288993
1.6167-1.65430.24041640.21532784294894
1.6543-1.69570.27521270.20632748287594
1.6957-1.74150.23031370.20822821295895
1.7415-1.79280.21031380.20222792293095
1.7928-1.85060.2051410.19972835297695
1.8506-1.91680.23081570.1872711286895
1.9168-1.99350.22391560.18292791294794
1.9935-2.08420.21961390.17412721286093
2.0842-2.1940.19321210.1742741286293
2.194-2.33150.18571340.17462833296797
2.3315-2.51140.22541540.17872826298097
2.5114-2.7640.1971480.192828297696
2.764-3.16360.24581660.18622801296796
3.1636-3.98430.17641700.16492647281791
3.9843-30.43120.18651340.17422474260885

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