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- PDB-3p8a: Crystal Structure of a hypothetical protein from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3p8a
TitleCrystal Structure of a hypothetical protein from Staphylococcus aureus
Componentsuncharacterized protein
KeywordsUNKNOWN FUNCTION / mainly antiparallel beta sheets / alpha and beta protein
Function / homology
Function and homology information


Immunoglobulin-like - #4320 / Glyoxalase-like domain / Glyoxalase-like domain / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glyoxalase-like domain protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsLam, R. / Qiu, W. / Battaile, K. / Lam, K. / Romanov, V. / Chan, T. / Pai, E. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal Structure of a hypothetical protein from Staphylococcus aureus
Authors: Qiu, W. / Lam, R. / Battaile, K. / Lam, K. / Romanov, V. / Chan, T. / Pai, E. / Chirgadze, N.Y.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,41714
Polymers65,1462
Non-polymers1,27212
Water5,044280
1
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1966
Polymers32,5731
Non-polymers6235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2218
Polymers32,5731
Non-polymers6497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.180, 49.730, 67.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein uncharacterized protein


Mass: 32572.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SA2664 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8KYA6

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Non-polymers , 5 types, 292 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 35.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 10 % PEG5KMME, 5 % Tacsimate, 0.1 M Bis-Tris, 0.01 M MgCl2, pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 37499 / Num. obs: 37456 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 18.56 Å2 / Rsym value: 0.0931 / Net I/σ(I): 17.4
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 5138 / Rsym value: 0.361 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→47.15 Å / Cor.coef. Fo:Fc: 0.9278 / Cor.coef. Fo:Fc free: 0.9012 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 1837 5.01 %RANDOM
Rwork0.2381 ---
obs0.2398 36674 --
Displacement parametersBiso mean: 23.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.6769 Å20 Å20 Å2
2--0.4378 Å20 Å2
3---0.2391 Å2
Refine analyzeLuzzati coordinate error obs: 0.303 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 80 280 4565
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0144182
X-RAY DIFFRACTIONt_angle_deg1.1759392
X-RAY DIFFRACTIONt_dihedral_angle_d16502
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1332
X-RAY DIFFRACTIONt_gen_planes6095
X-RAY DIFFRACTIONt_it441820
X-RAY DIFFRACTIONt_nbd25
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion19.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5595
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact51264
LS refinement shellResolution: 1.95→2.01 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2628 153 5.05 %
Rwork0.2553 2874 -
all0.2557 3027 -

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