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Basic information

Entry
Database: PDB / ID: 3lur
TitleCrystal structure of Putative bacterial transcription regulation protein (NP_372959.1) from Staphylococcus aureus MU50 at 1.81 A resolution
ComponentsPutative bacterial transcription regulation protein
KeywordsTranscription activator / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Bacterial transcription activator / effector binding domain
Function / homology
Function and homology information


: / Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily ...: / Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Bacterial transcription activator effector binding domain-containing protein / AraC_E_bind domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.81 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative bacterial transcription regulation protein (NP_372959.1) from Staphylococcus aureus MU50 at 1.81 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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 / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative bacterial transcription regulation protein
B: Putative bacterial transcription regulation protein
C: Putative bacterial transcription regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,02916
Polymers54,0463
Non-polymers98313
Water5,801322
1
A: Putative bacterial transcription regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5207
Polymers18,0151
Non-polymers5056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative bacterial transcription regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3085
Polymers18,0151
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative bacterial transcription regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2024
Polymers18,0151
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.179, 62.482, 105.075
Angle α, β, γ (deg.)90.000, 93.330, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILEAA4 - 165 - 17
21GLNGLNILEILEBB4 - 165 - 17
31GLNGLNILEILECC4 - 165 - 17
12ASNASNPROPROAA51 - 6352 - 64
22ASNASNPROPROBB51 - 6352 - 64
32ASNASNPROPROCC51 - 6352 - 64
13MSEMSEGLYGLYAA72 - 7773 - 78
23MSEMSEGLYGLYBB72 - 7773 - 78
33MSEMSEGLYGLYCC72 - 7773 - 78
14ASPASPGLUGLUAA87 - 10088 - 101
24ASPASPGLUGLUBB87 - 10088 - 101
34ASPASPGLUGLUCC87 - 10088 - 101
15ALAALAGLNGLNAA131 - 138132 - 139
25ALAALAGLNGLNBB131 - 138132 - 139
35ALAALAGLNGLNCC131 - 138132 - 139
16ILEILELYSLYSAA148 - 156149 - 157
26ILEILELYSLYSBB148 - 156149 - 157
36ILEILELYSLYSCC148 - 156149 - 157

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Components

#1: Protein Putative bacterial transcription regulation protein


Mass: 18015.416 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV2435 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q99RJ7, UniProt: A0A0H3K0Y5*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2000M NH4F, 20.0000% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97932,0.97949
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979491
ReflectionResolution: 1.81→29.192 Å / Num. obs: 39778 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.432 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.81-1.870.4211.991756412187.3
1.87-1.950.3052.5113247930194
1.95-2.040.2213.6109907638194.8
2.04-2.150.1654.6113397827196
2.15-2.280.1255.8106527291196.5
2.28-2.460.1066.8115427837196.7
2.46-2.70.0818.7108757337196.6
2.7-3.090.05112.4114047687196
3.09-3.890.0319.7110767454194.2
3.89-29.1920.02325112017438193.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→29.192 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.19 / SU B: 6.474 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. POLYETHYLENE GLYCOL (PG4 and PEG) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 4. ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 5.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2007 5 %RANDOM
Rwork0.176 ---
obs0.178 39762 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 49.12 Å2 / Biso mean: 15.582 Å2 / Biso min: 4.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20.69 Å2
2--0.07 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.81→29.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 64 322 4054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224045
X-RAY DIFFRACTIONr_bond_other_d0.0010.022698
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9575509
X-RAY DIFFRACTIONr_angle_other_deg0.75936693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.325541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.86526.263190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93815721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.348156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024565
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02754
X-RAY DIFFRACTIONr_mcbond_it0.5741.52446
X-RAY DIFFRACTIONr_mcbond_other0.1491.51005
X-RAY DIFFRACTIONr_mcangle_it1.0523971
X-RAY DIFFRACTIONr_scbond_it1.731599
X-RAY DIFFRACTIONr_scangle_it2.8164.51501
Refine LS restraints NCS

Ens-ID: 1 / Number: 711 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.360.5
2BMEDIUM POSITIONAL0.310.5
3CMEDIUM POSITIONAL0.360.5
1AMEDIUM THERMAL1.112
2BMEDIUM THERMAL0.782
3CMEDIUM THERMAL0.952
LS refinement shellResolution: 1.813→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 130 -
Rwork0.229 2731 -
all-2861 -
obs--98.69 %
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)
12.5465-0.22810.56030.947-0.26611.5734-0.0242-0.2030.01350.08940.0220.0305-0.02-0.01740.00220.03230.00130.01070.0183-0.00480.043322.48721.5336.119
21.6725-0.0983-0.220.7409-0.29070.99420.01840.0704-0.01090.0292-0.033-0.0518-0.05930.06250.01470.034-0.0042-0.00580.0443-0.00670.047727.48426.13939.867
31.0838-0.03140.02391.5917-0.32123.068-0.02850.03380.1079-0.1246-0.0675-0.02740.00480.10250.0960.049-0.00170.01080.05610.01080.091317.53254.76132.071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 157
2X-RAY DIFFRACTION2B0 - 157
3X-RAY DIFFRACTION3C0 - 157

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