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- PDB-6cul: PvdF of pyoverdin biosynthesis is a structurally unique N10-formy... -

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Basic information

Entry
Database: PDB / ID: 6cul
TitlePvdF of pyoverdin biosynthesis is a structurally unique N10-formyltetrahydrofolate-dependent formyltransferase
ComponentsPyoverdine synthetase F
KeywordsTRANSFERASE / N10-formyltetrahydrofolate-dependent formyltransferase
Function / homology
Function and homology information


formyl-CoA transferase activity / pyoverdine biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Formyl transferase, N-terminal domain superfamily
Similarity search - Domain/homology
CITRIC ACID / Chem-FGD / Pyoverdine synthetase F
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKenjic, N. / Hoag, M.R. / Moraski, G.C. / Caperelli, C.A. / Moran, G.R. / Lamb, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1403293 United States
CitationJournal: Arch. Biochem. Biophys. / Year: 2019
Title: PvdF of pyoverdin biosynthesis is a structurally unique N10-formyltetrahydrofolate-dependent formyltransferase.
Authors: Kenjic, N. / Hoag, M.R. / Moraski, G.C. / Caperelli, C.A. / Moran, G.R. / Lamb, A.L.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyoverdine synthetase F
B: Pyoverdine synthetase F
C: Pyoverdine synthetase F
D: Pyoverdine synthetase F
E: Pyoverdine synthetase F
F: Pyoverdine synthetase F
G: Pyoverdine synthetase F
H: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,72223
Polymers250,1098
Non-polymers4,61315
Water5,837324
1
A: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8953
Polymers31,2641
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4562
Polymers31,2641
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8953
Polymers31,2641
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8953
Polymers31,2641
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8953
Polymers31,2641
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8953
Polymers31,2641
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8953
Polymers31,2641
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Pyoverdine synthetase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8953
Polymers31,2641
Non-polymers6322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.988, 92.771, 127.579
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyoverdine synthetase F


Mass: 31263.629 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pvdF, PA2396 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I184
#2: Chemical
ChemComp-FGD / N-(4-{[(2-amino-4-oxo-1,4-dihydroquinazolin-6-yl)methyl]amino}benzene-1-carbonyl)-D-glutamic acid


Mass: 439.421 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H21N5O6
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.05 Å3/Da / Density % sol: 59.63 % / Description: Rectangular-prism, 0.15 m x 0.15 m x 0.04 m
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.55 M sodium citrate, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→38.76 Å / Num. obs: 121938 / % possible obs: 91.76 % / Observed criterion σ(F): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Rrim(I) all: 0.083 / Net I/σ(I): 9.1
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.87 / Rpim(I) all: 0.28 / Rrim(I) all: 0.398 / Rsym value: 0.398

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→38.76 Å / Cross valid method: FREE R-VALUE / σ(F): 0.43 / Phase error: 26.67 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 6618 5.43 %6147
Rwork0.2269 ---
obs0.2303 121938 91.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16952 0 328 324 17604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03717705
X-RAY DIFFRACTIONf_angle_d2.31324072
X-RAY DIFFRACTIONf_dihedral_angle_d16.14910407
X-RAY DIFFRACTIONf_chiral_restr0.1992558
X-RAY DIFFRACTIONf_plane_restr0.0133128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.34070.29233170.30275633X-RAY DIFFRACTION86
2.3407-2.38320.31353060.28545993X-RAY DIFFRACTION91
2.3832-2.4290.3153380.27995903X-RAY DIFFRACTION90
2.429-2.47860.30133090.28255947X-RAY DIFFRACTION90
2.4786-2.53250.27953070.27775864X-RAY DIFFRACTION89
2.5325-2.59140.24733100.27165902X-RAY DIFFRACTION89
2.5914-2.65620.29182730.27265782X-RAY DIFFRACTION88
2.6562-2.7280.29993270.26825681X-RAY DIFFRACTION86
2.728-2.80820.28172790.26035156X-RAY DIFFRACTION78
2.8082-2.89880.29013000.25315787X-RAY DIFFRACTION88
2.8988-3.00240.25993050.24555981X-RAY DIFFRACTION90
3.0024-3.12250.2792980.23235938X-RAY DIFFRACTION90
3.1225-3.26460.25663130.23735858X-RAY DIFFRACTION89
3.2646-3.43660.25342990.23135849X-RAY DIFFRACTION88
3.4366-3.65170.25522900.22855359X-RAY DIFFRACTION81
3.6517-3.93340.21753020.21375781X-RAY DIFFRACTION87
3.9334-4.32870.21233190.18985976X-RAY DIFFRACTION90
4.3287-4.95380.20563070.17045833X-RAY DIFFRACTION87
4.9538-6.23640.22033160.19295551X-RAY DIFFRACTION83
6.2364-37.07410.26013350.23675958X-RAY DIFFRACTION87

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