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- PDB-2ets: CRYSTAL STRUCTURE OF A BACTERIAL DOMAIN OF UNKNOWN FUNCTION FROM ... -

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Entry
Database: PDB / ID: 2ets
TitleCRYSTAL STRUCTURE OF A BACTERIAL DOMAIN OF UNKNOWN FUNCTION FROM DUF1798 FAMILY (MW1337) FROM STAPHYLOCOCCUS AUREUS SUBSP. AUREUS AT 2.25 A RESOLUTION
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


YppE-like / YppE-like / YppE-like superfamily / Bacterial domain of unknown function (DUF1798) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DUF1798 family protein / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2008
Title: Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold.
Authors: Kozbial, P. / Xu, Q. / Chiu, H.J. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Clayton, T. / Deller, M. / Duan, L. ...Authors: Kozbial, P. / Xu, Q. / Chiu, H.J. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Clayton, T. / Deller, M. / Duan, L. / Elias, Y. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kumar, A. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Reyes, R. / Rife, C.L. / Spraggon, G. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Wolf, G. / Zubieta, C. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN DATABASE. SEQUENCING CONFIRMED THAT ...SEQUENCE THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN DATABASE. SEQUENCING CONFIRMED THAT RESIDUE 45 IS ILE IN THIS STRAIN. THE ELECTRON DENSITY SUPPORTS THIS ASSIGNMENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6645
Polymers15,4631
Non-polymers2014
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)93,98530
Polymers92,7776
Non-polymers1,20824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area12500 Å2
ΔGint-295 kcal/mol
Surface area29670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.473, 93.473, 101.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-138-

HOH

21A-144-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

#1: Protein hypothetical protein


Mass: 15462.802 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: np_646154.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NWP7, UniProt: A0A0H3JWF6*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 0.2M MgCl2, 2.5M NaCl, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2005 / Details: Adjustable focusing mirrors. K-B geometry
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.25→29.29 Å / Num. obs: 8245 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.25-2.3110015.30.9760.75960.976
2.31-2.3710015.20.75615890.756
2.37-2.4410015.30.571.35780.57
2.44-2.5210015.30.5071.55460.507
2.52-2.610015.20.4071.85440.407
2.6-2.6910015.20.35915180.359
2.69-2.7910015.30.2932.54970.293
2.79-2.910015.10.2243.25010.224
2.9-3.0310015.30.1883.84550.188
3.03-3.1810015.20.1544.64540.154
3.18-3.35100150.1285.24210.128
3.35-3.5610014.90.1076.13950.107
3.56-3.810014.90.0996.33770.099
3.8-4.1110014.60.0966.83590.096
4.11-4.510014.30.0847.43320.084
4.5-5.0310014.40.0817.52970.081
5.03-5.8110014.40.0896.52740.089
5.81-7.12100140.0946.82270.094
7.12-10.0610013.50.0797.21780.079
10.06-29.2996.911.70.07971070.079

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→29.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.573 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.179
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). POOR DEFINED DENSITY A -4 TO A -1. 3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). POOR DEFINED DENSITY A -4 TO A -1. 3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4). THE ARG 85 SIDE CHAIN IS LOCATED ON THE 2-FOLD AXIS AND IS DISORDERED. ARG 85 WITHOUT SIDE CHAIN BEYOND BETA CARBON IS MODELED. 5). THE CHLORIDE AND PHOSPHATE IONS ARE TENATIVELY MODELLED ACCORDING ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 382 4.6 %RANDOM
Rwork0.175 ---
all0.177 ---
obs-7863 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.769 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0.67 Å20 Å2
2---1.34 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 8 55 1012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022977
X-RAY DIFFRACTIONr_bond_other_d0.0010.02854
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.941320
X-RAY DIFFRACTIONr_angle_other_deg0.80431997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34825.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08315182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.441153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_nbd_refined0.2290.2249
X-RAY DIFFRACTIONr_nbd_other0.1740.2834
X-RAY DIFFRACTIONr_nbtor_refined0.190.2479
X-RAY DIFFRACTIONr_nbtor_other0.0880.2491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.25
X-RAY DIFFRACTIONr_mcbond_it2.2023632
X-RAY DIFFRACTIONr_mcbond_other0.533232
X-RAY DIFFRACTIONr_mcangle_it3.1965938
X-RAY DIFFRACTIONr_scbond_it6.7368431
X-RAY DIFFRACTIONr_scangle_it8.20511381
LS refinement shellResolution: 2.251→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 31 -
Rwork0.208 566 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 20.065 Å / Origin y: 53.841 Å / Origin z: 27.236 Å
111213212223313233
T-0.2368 Å2-0.0135 Å2-0.1507 Å2-0.0684 Å2-0.1953 Å2---0.1926 Å2
L4.3636 °20.3765 °20.5765 °2-6.5572 °20.7858 °2--2.2547 °2
S0.2543 Å °-0.6654 Å °-0.0666 Å °0.3507 Å °0.1241 Å °-0.6192 Å °0.1011 Å °0.4803 Å °-0.3784 Å °

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