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- PDB-2ark: Structure of a flavodoxin from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2ark
TitleStructure of a flavodoxin from Aquifex aeolicus
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / flavodoxin / Aquifex aeolicus / FMN / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Flavodoxin
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCuff, M.E. / Quartey, P. / Zhou, M. / Cymborowski, M. / Minor, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a flavodoxin from Aquifex aeolicus
Authors: Cuff, M.E. / Quartey, P. / Zhou, M. / Cymborowski, M. / Minor, W. / Joachimiak, A.
History
DepositionAug 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE:1, 2 This entry contains the crystallographic asymmetric unit which consists of 6 ...BIOMOLECULE:1, 2 This entry contains the crystallographic asymmetric unit which consists of 6 chain(s). See remark 350 for information on generating the biological molecule(s). According to authors, the biological unit is not known but most likely a tetramer.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
C: Flavodoxin
D: Flavodoxin
E: Flavodoxin
F: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,55518
Polymers126,4336
Non-polymers1,12212
Water7,566420
1
A: Flavodoxin
B: Flavodoxin
C: Flavodoxin
D: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,22114
Polymers84,2884
Non-polymers93210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14580 Å2
ΔGint-113 kcal/mol
Surface area23780 Å2
MethodPISA
2
E: Flavodoxin
F: Flavodoxin
hetero molecules

E: Flavodoxin
F: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6688
Polymers84,2884
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)112.846, 112.846, 150.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsUnknown, but most likely the tetramer A,B,C,D.

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Components

#1: Protein
Flavodoxin /


Mass: 21072.107 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: fldA, floX / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67866
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na-HEPES, Na Citrate, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911, 0.97924
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 6, 2005 / Details: SBC3
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.979241
ReflectionResolution: 2.4→36 Å / Num. all: 43827 / Num. obs: 43827 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.72 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXphasing
RESOLVEphasing
DMphasing
Cootmodel building
Omodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.4→36 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.522 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.559 / ESU R Free: 0.269
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23519 2202 5 %RANDOM
Rwork0.17079 ---
all0.17396 43765 --
obs0.17396 41563 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.432 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.9 Å20 Å2
2--1.79 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8633 0 66 420 9119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228843
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.96211878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9951110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9623.156377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.392151585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9421572
X-RAY DIFFRACTIONr_chiral_restr0.1370.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026530
X-RAY DIFFRACTIONr_nbd_refined0.2080.24473
X-RAY DIFFRACTIONr_nbtor_refined0.3020.25937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2499
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.233
X-RAY DIFFRACTIONr_mcbond_it0.9681.55599
X-RAY DIFFRACTIONr_mcangle_it1.24928671
X-RAY DIFFRACTIONr_scbond_it2.70633748
X-RAY DIFFRACTIONr_scangle_it3.6314.53207
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 149 -
Rwork0.225 3031 -
obs--99.34 %
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)
12.17260.42540.27671.9199-0.22912.83790.0423-0.08530.18680.0931-0.00070.1025-0.3235-0.2397-0.0416-0.09980.04740.0169-0.1692-0.0117-0.1998101.972777.994268.4892
21.93730.2688-0.57451.97520.26762.8169-0.02520.24960.0471-0.24360.05170.1384-0.0145-0.3803-0.0265-0.1622-0.0221-0.0866-0.0230.0248-0.211295.991367.037648.0485
32.34910.14650.04971.76380.49893.67120.11640.0159-0.49540.13120.0232-0.1310.75280.298-0.13960.05860.0899-0.0849-0.1541-0.0107-0.0401117.999349.192362.9077
41.70560.3430.98121.856-0.19373.26950.02820.33-0.042-0.1920.0434-0.2748-0.0970.8063-0.0716-0.2038-0.0530.04210.1568-0.0694-0.1042129.053968.417853.5126
53.1924-0.5267-0.72652.5438-0.02383.4315-0.0393-0.21920.67830.14170.0768-0.5851-0.17360.6038-0.0375-0.1993-0.0796-0.0228-0.0178-0.10610.173772.0786102.703680.0249
62.8861-0.63490.00762.4274-0.56813.15920.04110.3611-0.1476-0.2152-0.02730.03820.4958-0.0455-0.0138-0.009-0.05060.057-0.1725-0.0838-0.187854.075681.046565.1059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 1841 - 187
2X-RAY DIFFRACTION1AG5011
3X-RAY DIFFRACTION2BB-1 - 1842 - 187
4X-RAY DIFFRACTION2BH5021
5X-RAY DIFFRACTION3CC0 - 1853 - 188
6X-RAY DIFFRACTION3CI5031
7X-RAY DIFFRACTION4DD-2 - 1841 - 187
8X-RAY DIFFRACTION4DJ5041
9X-RAY DIFFRACTION5EE1 - 1854 - 188
10X-RAY DIFFRACTION5EK5051
11X-RAY DIFFRACTION6FF0 - 1843 - 187
12X-RAY DIFFRACTION6FL5061

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