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- PDB-2nyd: Crystal structure of Staphylococcus aureus hypothetical protein SA1388 -

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Basic information

Entry
Database: PDB / ID: 2nyd
TitleCrystal structure of Staphylococcus aureus hypothetical protein SA1388
ComponentsUPF0135 protein SA1388
KeywordsUNKNOWN FUNCTION / HYPOTHETICAL PROTEIN SA1388 / SELENOMETHIONINE SAD
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
Rubrerythrin, domain 2 - #300 / DUF34/NIF3, bacteria / DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / Alpha-Beta Plaits - #120 / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Rubrerythrin, domain 2 / Single Sheet / Alpha-Beta Plaits ...Rubrerythrin, domain 2 - #300 / DUF34/NIF3, bacteria / DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / Alpha-Beta Plaits - #120 / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Rubrerythrin, domain 2 / Single Sheet / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GTP cyclohydrolase 1 type 2 homolog
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSingh, K.S. / Zhang, X. / Zhang, H.
CitationJournal: Bmc Struct.Biol. / Year: 2006
Title: Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center.
Authors: Singh Saikatendu, K. / Zhang, X. / Kinch, L. / Leybourne, M. / Grishin, N.V. / Zhang, H.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE AUTHORS STATE THAT G32E MUTATION IS INCIDENTAL DUE TO PCR, AND THAT A115V MUTATION MIGHT ... SEQUENCE AUTHORS STATE THAT G32E MUTATION IS INCIDENTAL DUE TO PCR, AND THAT A115V MUTATION MIGHT BE INCIDENTAL, EITHER DUE TO PCR OR ARISEN SPONTANEOUSLY. AUTHORS CLEARLY SEE THE ELECTRON DENSITY FOR RESIDUE 115 AND THEREFORE MODELED THIS RESIDUE AS VALINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5246
Polymers83,2622
Non-polymers2624
Water15,295849
1
A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules

A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules

A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,57218
Polymers249,7876
Non-polymers78512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area22410 Å2
ΔGint-535 kcal/mol
Surface area81210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.547, 132.547, 125.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

DetailsHEXAMER. THE FUNCTIONAL OLIGOMER IS MOST LIKELY A HEXAMER FORMED BY A DIMER OF TRIMERS

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Components

#1: Protein UPF0135 protein SA1388


Mass: 41631.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: N315 / Gene: SA1388 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67273
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Description: The structure factor file that authors deposited is the native data set used in the refinement
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bis-Tris propane, pH 8.5, 0.2 M MgCl2, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2004 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→84.51 Å / Num. all: 50416 / Num. obs: 50416 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.05 / Net I/σ(I): 18.01
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 1.96 / Rsym value: 0.249 / % possible all: 73.76

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→84.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.466 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SAD DATA SET HAS BEEN USED FOR PHASING, AND THE NATIVE DATA SET HAS BEEN USED FOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2661 5 %RANDOM
Rwork0.17314 ---
obs0.17605 50201 94.98 %-
all-50201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.059 Å
Luzzati d res low-6 Å
Luzzati sigma a0.46 Å0.292 Å
Refinement stepCycle: LAST / Resolution: 2→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 4 849 5923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9527008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.34726.245237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7615914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.405157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023855
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22600
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23569
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2686
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.051.53353
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64225203
X-RAY DIFFRACTIONr_scbond_it2.56932094
X-RAY DIFFRACTIONr_scangle_it3.8194.51805
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 147 -
Rwork0.198 2974 -
obs--75.15 %

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