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- PDB-3frm: The crystal structure of a functionally unknown conserved protein... -

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Basic information

Entry
Database: PDB / ID: 3frm
TitleThe crystal structure of a functionally unknown conserved protein from Staphylococcus epidermidis ATCC 12228.
Componentsuncharacterized conserved protein
Keywordsstructural genomics / unknown function / APC61048 / conserved protein / Staphylococcus epidermidis ATCC 12228 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Domain of unknown function DUF5613 / Domain of unknown function (DUF5613) / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyltransferase domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsTan, K. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown conserved protein from Staphylococcus epidermidis ATCC 12228.
Authors: Tan, K. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein
E: uncharacterized conserved protein
F: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,28523
Polymers178,7936
Non-polymers1,49217
Water5,639313
1
A: uncharacterized conserved protein
B: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9327
Polymers59,5982
Non-polymers3345
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-83 kcal/mol
Surface area23910 Å2
MethodPISA
2
C: uncharacterized conserved protein
D: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9327
Polymers59,5982
Non-polymers3345
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-87 kcal/mol
Surface area24140 Å2
MethodPISA
3
E: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2095
Polymers29,7991
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2124
Polymers29,7991
Non-polymers4133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.711, 126.549, 112.807
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211
DetailsEXPERIMENTALLY UNKNOWN. IT IS PREDICTED THAT THE CHAINS A AND B, AND C AND D FORM PSEUDO 2-FOLD DIMERS RESPECTIVELY. THE CHAINS E AND F SEEM TO BE MONOMERIC.

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Components

#1: Protein
uncharacterized conserved protein


Mass: 29798.752 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE_1855, Staphylococcus epidermidis / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8CRE9, UniProt: A0A0H2VHN1*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Li2SO4, 0.1M Acetate, 2.5M NaCl, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2008 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.32→42 Å / Num. all: 76418 / Num. obs: 76418 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 16.5
Reflection shellResolution: 2.33→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.71 / Num. unique all: 3866 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→41.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 19.537 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.363 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26346 3823 5 %RANDOM
Rwork0.19667 ---
all0.20003 72287 --
obs0.20003 72287 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.447 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0.16 Å2
2--0.92 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.32→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12376 0 82 313 12771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.96417233
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36651519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57124.929631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.452152328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0921555
X-RAY DIFFRACTIONr_chiral_restr0.1350.21871
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219589
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.57560
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.575212270
X-RAY DIFFRACTIONr_scbond_it2.84435183
X-RAY DIFFRACTIONr_scangle_it4.3624.54958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.322→2.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 259 -
Rwork0.239 4886 -
obs-5145 91.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.03810.18160.31781.56070.29040.8724-0.00230.06430.0251-0.13970.0573-0.1375-0.11130.0884-0.0550.0886-0.01820.02630.01130.00130.409255.15886.10971.023
20.7540.3133-0.08881.0974-0.34251.16250.01720.02760.08110.16010.037-0.0076-0.15520.1-0.05420.18820.00320.03010.0146-0.01760.464149.43696.62299.07
31.3603-0.20460.49470.97170.04052.02810.06850.0816-0.04-0.08250.0104-0.0531-0.02250.2601-0.07890.1592-0.05580.00360.0579-0.05920.460420.943127.50671.174
41.4042-0.2357-0.28321.48530.32110.66190.01750.0442-0.06740.2121-0.0435-0.04330.13560.00980.0260.1828-0.051-0.00130.0235-0.0160.391722.171138.36999.729
50.7073-0.48040.09471.60340.43461.8431-0.0989-0.0423-0.09120.15980.1189-0.01460.14750.1832-0.020.09970.02510.03170.0250.03090.51555.91657.59391.446
62.01741.2580.60392.54090.64791.4743-0.07560.32010.1147-0.08590.20870.0437-0.08980.3683-0.13310.0863-0.0354-0.00320.11430.02430.503624.80141.05379.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 251
2X-RAY DIFFRACTION2B0 - 251
3X-RAY DIFFRACTION3C-2 - 251
4X-RAY DIFFRACTION4D-1 - 251
5X-RAY DIFFRACTION5E0 - 251
6X-RAY DIFFRACTION6F0 - 251

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