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- PDB-1t5b: Structural genomics, A protein from Salmonella typhimurium simila... -

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Basic information

Entry
Database: PDB / ID: 1t5b
TitleStructural genomics, A protein from Salmonella typhimurium similar to E. coli acyl carrier protein phosphodiesterase
ComponentsAcyl carrier protein phosphodiesterase
KeywordsHYDROLASE / structural genomics / acyl carrier protein phosphodiesterase / FMN / Alpha/beta/alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsZhang, R. / Wu, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.4 A crystal structure of a protein from Salmonella typhimurium similar to E. coli acyl carrier protein phosphodiesterase
Authors: Zhang, R. / Wu, R. / Collart, F. / Joachimiak, A.
History
DepositionMay 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Acyl carrier protein phosphodiesterase
B: Acyl carrier protein phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2124
Polymers43,3002
Non-polymers9132
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-35 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.891, 107.915, 51.168
Angle α, β, γ (deg.)90.00, 111.45, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein exists as dimer. MolA and MolB represent the dimer in the asymmtric unit

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Components

#1: Protein Acyl carrier protein phosphodiesterase / ACP phosphodiesterase


Mass: 21649.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: ACPD, STM1642, STY1427, T1545 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P63462, [acyl-carrier-protein] phosphodiesterase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.42 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% Glycerol, 20.5% PEG 4000, 0.065 M tris-sodium Citrate, 0.1 M NH4 acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Feb 25, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 1.4→50 Å / Num. all: 160508 / Num. obs: 164570 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 32.07
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 4.63 / Num. unique all: 12710

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→30.55 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 405562.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 7555 5 %RANDOM
Rwork0.196 ---
all0.205 160796 --
obs0.196 151470 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.4165 Å2 / ksol: 0.41075 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å21.17 Å2
2---0.78 Å20 Å2
3----1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.4→30.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 62 392 3477
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 1031 4.9 %
Rwork0.257 19937 -
obs--78.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4FMN.PARAM

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