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- PDB-2fzv: Crystal Structure of an apo form of a Flavin-binding Protein from... -

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Basic information

Entry
Database: PDB / ID: 2fzv
TitleCrystal Structure of an apo form of a Flavin-binding Protein from Shigella flexneri
Componentsputative arsenical resistance protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Flavin binding Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


azobenzene reductase activity / FMN reductase (NADPH) activity / : / Oxidoreductases / FMN binding / protein homotetramerization
Similarity search - Function
Arsenate resistance ArsH / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NADPH-dependent FMN reductase ArsH
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsVorontsov, I.I. / Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structure of an apo form of Shigella flexneri ArsH protein with an NADPH-dependent FMN reductase activity
Authors: Vorontsov, I.I. / Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Kiryukhina, O. / Collart, F.R. / Anderson, W.F.
History
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _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: putative arsenical resistance protein
B: putative arsenical resistance protein
C: putative arsenical resistance protein
D: putative arsenical resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8287
Polymers124,7174
Non-polymers1113
Water20,0151111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-64 kcal/mol
Surface area37160 Å2
MethodPISA
2
A: putative arsenical resistance protein
B: putative arsenical resistance protein
C: putative arsenical resistance protein
D: putative arsenical resistance protein
hetero molecules

A: putative arsenical resistance protein
B: putative arsenical resistance protein
C: putative arsenical resistance protein
D: putative arsenical resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,65614
Polymers249,4348
Non-polymers2226
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area26230 Å2
ΔGint-163 kcal/mol
Surface area72800 Å2
MethodPISA
3
A: putative arsenical resistance protein
C: putative arsenical resistance protein
hetero molecules

A: putative arsenical resistance protein
C: putative arsenical resistance protein
hetero molecules

B: putative arsenical resistance protein
D: putative arsenical resistance protein

B: putative arsenical resistance protein
D: putative arsenical resistance protein


Theoretical massNumber of molelcules
Total (without water)249,65614
Polymers249,4348
Non-polymers2226
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation4_455y-1/2,-x+1/2,z+1/41
crystal symmetry operation5_545-x+1/2,y-1/2,-z+3/41
Buried area22730 Å2
ΔGint-168 kcal/mol
Surface area76300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.821, 117.821, 154.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsChains A,B,C, and D represent biological assembly, which is homo-tetramer.

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Components

#1: Protein
putative arsenical resistance protein


Mass: 31179.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Species: Shigella flexneri / Strain: 2457T / Gene: AAP17869 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: GenBank: 30042143, UniProt: Q7UC03*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1111 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M Calcium chloride dihydrate, 20% w/v Polyethylene glycol 3350, 0.5 M NaCl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 5ID-B10.94644
SYNCHROTRONAPS 8-BM20.97949
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDNov 27, 2005Mirrors
ADSC QUANTUM 42CCDDec 11, 2005Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946441
20.979491
ReflectionResolution: 1.7→29.81 Å / Num. all: 116180 / Num. obs: 116180 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 38.33
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.68 / Num. unique all: 17520 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→29.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.595 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Atomic isotropic B-factor refinement
Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.121 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24579 5843 5 %RANDOM
Rwork0.1988 ---
all0.20116 110950 --
obs0.20116 110950 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7522 0 3 1111 8636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0218198
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.96711165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.42251046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.06422.199391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.117151401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.60115104
X-RAY DIFFRACTIONr_chiral_restr0.0910.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026457
X-RAY DIFFRACTIONr_nbd_refined0.1950.24397
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21013
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.244
X-RAY DIFFRACTIONr_mcbond_it1.1331.55295
X-RAY DIFFRACTIONr_mcangle_it1.59528275
X-RAY DIFFRACTIONr_scbond_it2.57333287
X-RAY DIFFRACTIONr_scangle_it3.6024.52890
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 408 -
Rwork0.325 7798 -
obs-7798 94.94 %
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)
11.4536-0.2874-0.38281.5632-0.21491.9757-0.00620.08370.06980.023-0.00250.0785-0.0644-0.09550.0088-0.23890.01890.0038-0.2471-0.0167-0.245622.584822.893261.1305
21.36170.3736-0.17272.73140.07492.5441-0.09880.10480.0351-0.24280.06380.2477-0.0668-0.22060.035-0.10030.0022-0.0217-0.24560.0134-0.161617.433843.565534.0121
31.701-0.1492-0.51361.35880.50122.6801-0.01910.2823-0.1604-0.16340.0175-0.09440.28670.36050.0016-0.16190.07920.0064-0.0814-0.0429-0.191843.704211.245145.0735
42.02730.4595-0.15742.709-0.28872.4031-0.20520.4551-0.5137-0.54540.0994-0.00430.48280.02330.10590.1584-0.04560.0424-0.0761-0.13310.044317.912422.685918.912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 23323 - 257
2X-RAY DIFFRACTION2BB0 - 24624 - 270
3X-RAY DIFFRACTION3CC-8 - 23116 - 255
4X-RAY DIFFRACTION4DD1 - 24225 - 266

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