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- PDB-2qgs: Crystal structure of SE1688 protein from Staphylococcus epidermid... -

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Basic information

Entry
Database: PDB / ID: 2qgs
TitleCrystal structure of SE1688 protein from Staphylococcus epidermidis. Northeast Structural Genomics Consortium target SeR89
ComponentsProtein SE1688
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-helical protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


HD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / HD domain / HD domain / Cyclin A; domain 1 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Su, M. / Benach, J. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Owen, L. / Ma, L.-C. / Xiao, R. ...Forouhar, F. / Su, M. / Benach, J. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Owen, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of SE1688 protein from Staphylococcus epidermidis.
Authors: Forouhar, F. / Su, M. / Benach, J. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Owen, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, ...Authors: Forouhar, F. / Su, M. / Benach, J. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Owen, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SE1688
B: Protein SE1688
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8254
Polymers53,6942
Non-polymers1312
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-92 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.736, 62.843, 71.828
Angle α, β, γ (deg.)90.00, 107.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein SE1688


Mass: 26847.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE_1688 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8CRP0, UniProt: A0A0H2VIU2*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7
Details: Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Reservoir solution: 100 mM MOPS pH 7.0, 20% PEG 1000, 100 mM Sodium bromide, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→28.56 Å / Num. all: 63279 / Num. obs: 63279 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.045 / Net I/σ(I): 26.75
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.04 / Rsym value: 0.148 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→28.56 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 494204.78 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: THE FRIEDEL PAIRS WERE USED FOR PHASING. XtalView program has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5563 9.9 %RANDOM
Rwork0.208 ---
obs0.208 56428 88.3 %-
all-63279 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.8689 Å2 / ksol: 0.407495 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0.34 Å2
2---2.57 Å20 Å2
3---2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 2 410 3775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 489 9.3 %
Rwork0.202 4759 -
obs--81.5 %

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