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- PDB-3k9r: X-ray structure of the Rhodanese-like domain of the Alr3790 prote... -

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Basic information

Entry
Database: PDB / ID: 3k9r
TitleX-ray structure of the Rhodanese-like domain of the Alr3790 protein from Anabaena sp. Northeast Structural Genomics Consortium Target NsR437c.
ComponentsAlr3790 protein
Keywordsstructural genomics / unknown function / ALR3790 / RHODANESE-LIKE / NSR437C / NESG / STRUCTURAL GENOMICS. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsVorobiev, S. / Chen, Y. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S. / Chen, Y. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray structure of the Rhodanese-like domain of the Alr3790 protein from Anabaena sp.
Authors: Vorobiev, S. / Chen, Y. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 6, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alr3790 protein
B: Alr3790 protein
C: Alr3790 protein
D: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)51,7314
Polymers51,7314
Non-polymers00
Water5,206289
1
A: Alr3790 protein
B: Alr3790 protein

C: Alr3790 protein
D: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)51,7314
Polymers51,7314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area9250 Å2
ΔGint-52 kcal/mol
Surface area16750 Å2
MethodPISA
2
A: Alr3790 protein
B: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)25,8662
Polymers25,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-13 kcal/mol
Surface area10270 Å2
MethodPISA
3
A: Alr3790 protein

C: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)25,8662
Polymers25,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area1840 Å2
ΔGint-10 kcal/mol
Surface area11520 Å2
MethodPISA
4
B: Alr3790 protein

D: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)25,8662
Polymers25,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area1430 Å2
ΔGint-9 kcal/mol
Surface area11200 Å2
MethodPISA
5
C: Alr3790 protein
D: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)25,8662
Polymers25,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-15 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.286, 78.894, 64.767
Angle α, β, γ (deg.)90.00, 103.09, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer according to aggregation screening; however likely dimer under crystallization conditions.

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Components

#1: Protein
Alr3790 protein


Mass: 12932.752 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr3790 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) +MAGIC / References: UniProt: Q8YQN0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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

Crystal growTemperature: 291 K / Method: microbatch under parafin oil / pH: 4.5
Details: 25% PEG 3350, 0.1M sodium acetate, pH 4.5, MICROBATCH UNDER PARAFIN OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 9, 2009 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 52885 / Num. obs: 49871 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.6
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5315 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ILM

3ilm


Resolution: 1.96→36.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 382449.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2145 4.8 %RANDOM
Rwork0.203 ---
obs0.203 44270 85.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1714 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.89 Å20 Å20.47 Å2
2---0.8 Å20 Å2
3----7.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.96→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 0 289 3342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.71
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.96→2.08 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 312 4.8 %
Rwork0.211 6180 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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