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- PDB-4pau: Hypothetical protein SA1058 from S. aureus. -

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Basic information

Entry
Database: PDB / ID: 4pau
TitleHypothetical protein SA1058 from S. aureus.
ComponentsNitrogen regulatory protein A
KeywordsUNKNOWN FUNCTION / hypothetical protein
Function / homologyGAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / : / GAF domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsBattaile, K.P. / Wu-Brown, J. / Romanov, V. / Jones, K. / Lam, R. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To Be Published
Title: Hypothetical protein SA1058 from S. aureus.
Authors: Battaile, K.P. / Lam, R. / Wu-Brown, J. / Romanov, V. / Jones, K. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.pdbx_collection_date ..._citation.journal_id_CSD / _diffrn_detector.pdbx_collection_date / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogen regulatory protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3512
Polymers17,3161
Non-polymers351
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.870, 36.050, 38.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nitrogen regulatory protein A


Mass: 17315.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: N6ELX6, UniProt: Q2FVM5*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 28% PEG 2000MME, 0.1M bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791941 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791941 Å / Relative weight: 1
ReflectionResolution: 2→54.44 Å / Num. obs: 16151 / % possible obs: 98 % / Redundancy: 7.2 % / Biso Wilson estimate: 47.08 Å2 / Net I/σ(I): 199

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2→54.44 Å / Cor.coef. Fo:Fc: 0.9516 / Cor.coef. Fo:Fc free: 0.9391 / SU R Cruickshank DPI: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.258 493 4.69 %RANDOM
Rwork0.2024 ---
obs0.2052 10509 97.63 %-
Displacement parametersBiso mean: 67.66 Å2
Baniso -1Baniso -2Baniso -3
1-5.017 Å20 Å20 Å2
2---1.4384 Å20 Å2
3----3.5786 Å2
Refine analyzeLuzzati coordinate error obs: 0.323 Å
Refinement stepCycle: 1 / Resolution: 2→54.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 1 20 1023
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011026HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.041384HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d368SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes20HARMONIC2
X-RAY DIFFRACTIONt_gen_planes149HARMONIC5
X-RAY DIFFRACTIONt_it1026HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion15.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion127SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1179SEMIHARMONIC4
LS refinement shellResolution: 2→2.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2391 126 4.45 %
Rwork0.1898 2704 -
all0.1919 2830 -
obs--97.63 %
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)
17.4161.7731.10546.22420.52928.20410.0359-1.6327-0.33740.8653-0.1180.11150.0479-0.17990.0822-0.3282-0.0463-0.0131-0.0730.0574-0.16315.56114.722137.0309
24.0737-0.74613.414100.42131.4740.00650.81430.1578-0.67990.07250.4762-0.1733-0.4185-0.079-0.1954-0.0136-0.30870.03650.20930.74230.000211.847221.919
310.48972.6044-0.33438.82982.47382.90620.2677-0.40020.8574-0.2296-0.02630.323-0.71230.0325-0.2414-0.2423-0.0308-0.0063-0.2906-0.0650.016915.808113.50229.7261
40.1316-0.28745.06480.00631.18815.59160.07981.01830.361-0.52530.21440.4364-0.1913-0.8584-0.2941-0.1021-0.083-0.08310.08750.00180.220710.35119.263517.4228
50-7.97443.65479.9945-8.40575.2232-0.18510.527-0.2504-0.30990.14460.0833-0.1589-0.02960.0406-0.2259-0.0394-0.0678-0.0096-0.12190.043811.26760.846620.0984
610.86381.3319-3.40850.41330.86182.7992-0.01620.27770.0893-0.2568-0.34530.04650.45650.02540.3615-0.2791-0.05580.0662-0.3686-0.11380.374620.1888-4.269422.5437
74.1827-8.0019-1.93463.63871.47895.15350.14740.1734-0.0971-0.7324-0.393-0.5180.0208-0.50540.2456-0.2108-0.00750.0369-0.2817-0.0510.243426.51265.53715.1159
89.95771.4144-1.543.8625-1.03452.50620.1316-0.3277-0.753-0.0877-0.1532-0.0951-0.0074-0.0530.0216-0.3043-0.023-0.0477-0.266-0.03420.039615.93512.354426.4123
96.54345.00721.82435.39211.05272.02890.1275-0.2788-0.35020.2764-0.12160.24590.17-0.1082-0.0058-0.3063-0.0338-0.017-0.19090.0190.096612.94960.955129.4302
100-2.3668-0.19193.82911.631810.8462-0.1292-1.1124-0.31660.61160.1258-0.30040.57510.85820.0034-0.25470.0516-0.0788-0.0080.09650.348128.8688-0.954231.346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|10 - 33}
2X-RAY DIFFRACTION2{A|34 - 41}
3X-RAY DIFFRACTION3{A|42 - 57}
4X-RAY DIFFRACTION4{A|58 - 64}
5X-RAY DIFFRACTION5{A|65 - 73}
6X-RAY DIFFRACTION6{A|74 - 81}
7X-RAY DIFFRACTION7{A|82 - 93}
8X-RAY DIFFRACTION8{A|94 - 114}
9X-RAY DIFFRACTION9{A|115 - 124}
10X-RAY DIFFRACTION10{A|125 - 133}

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