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- PDB-2nxo: Crystal structure of protein SCO4506 from Streptomyces coelicolor... -

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Basic information

Entry
Database: PDB / ID: 2nxo
TitleCrystal structure of protein SCO4506 from Streptomyces coelicolor, Pfam DUF178
ComponentsHypothetical protein SCO4506Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pfam / DUf178 / NYSGXRC / 10093f / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


chorismate dehydratase / menaquinone biosynthetic process / hydro-lyase activity
Similarity search - Function
Chorismate dehydratase / Menaquinone biosynthesis enzyme / Menaquinone biosynthesis / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chorismate dehydratase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsTyagi, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of a hypothetical protein SCO4506 (gene ID: Q9L0T8) from Streptomyces coelicolor to 2.04 Angstrom resolution
Authors: Tyagi, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein SCO4506
B: Hypothetical protein SCO4506
C: Hypothetical protein SCO4506
D: Hypothetical protein SCO4506


Theoretical massNumber of molelcules
Total (without water)129,8994
Polymers129,8994
Non-polymers00
Water9,908550
1
A: Hypothetical protein SCO4506
D: Hypothetical protein SCO4506


Theoretical massNumber of molelcules
Total (without water)64,9502
Polymers64,9502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein SCO4506
C: Hypothetical protein SCO4506


Theoretical massNumber of molelcules
Total (without water)64,9502
Polymers64,9502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-6 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.792, 97.370, 86.570
Angle α, β, γ (deg.)90.00, 106.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical protein SCO4506 / Hypothesis


Mass: 32474.861 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: Q9L0T8 / Plasmid: T7 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9L0T8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X2510.9798
SYNCHROTRONNSLS X29A20.9791
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 6, 2006Mirrors
ADSC QUANTUM 3152CCDSep 1, 2006Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(III)SINGLE WAVELENGTHMx-ray1
2Si(III)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.97911
ReflectionResolution: 2.04→50 Å / Num. all: 76032 / Num. obs: 76032 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.209 / Num. unique all: 6908 / % possible all: 89.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SHELXDphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.04→30.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 81815.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The missing residues listed in Remark 465 are due to lack of density. Residues listed having missing atoms in Remark 470 were modeled as ALA due to weak or lack of electron density. ...Details: The missing residues listed in Remark 465 are due to lack of density. Residues listed having missing atoms in Remark 470 were modeled as ALA due to weak or lack of electron density. Continuous residual density in the electron density map which may be due to unidentifiable substrate was modeled with a few waters. This was present in all four monomers.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2264 3.1 %RANDOM
Rwork0.249 ---
all0.263 ---
obs0.249 71996 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1264 Å2 / ksol: 0.328717 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å2-2.71 Å2
2--3.56 Å20 Å2
3----1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.04→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8150 0 0 550 8700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 308 3.1 %
Rwork0.267 9441 -
obs-10182 76.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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