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- PDB-3bdd: CRYSTAL STRUCTURE OF A PUTATIVE MULTIPLE ANTIBIOTIC-RESISTANCE RE... -

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Entry
Database: PDB / ID: 3bdd
TitleCRYSTAL STRUCTURE OF A PUTATIVE MULTIPLE ANTIBIOTIC-RESISTANCE REPRESSOR (SSU05_1136) FROM STREPTOCOCCUS SUIS 89/1591 AT 2.20 A RESOLUTION
ComponentsRegulatory protein MarR
KeywordsTRANSCRIPTION / PUTATIVE MULTIPLE ANTIBIOTIC-RESISTANCE REPRESSOR / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 / DNA-BINDING / TRANSCRIPTION REGULATION
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / PHOSPHATE ION / :
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative multiple antibiotic-resistance repressor (MarR) (ZP_00875883.1) from Streptococcus suis 89/1591 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 1.4Jan 25, 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein MarR
B: Regulatory protein MarR
C: Regulatory protein MarR
D: Regulatory protein MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,55210
Polymers65,9944
Non-polymers5586
Water4,035224
1
A: Regulatory protein MarR
B: Regulatory protein MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3716
Polymers32,9972
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
MethodPISA
2
C: Regulatory protein MarR
D: Regulatory protein MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1814
Polymers32,9972
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.734, 100.430, 68.695
Angle α, β, γ (deg.)90.000, 111.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUARGAA3 - 764 - 77
21GLUARGBB3 - 764 - 77
31GLUARGCC3 - 764 - 77
41GLUARGDD3 - 764 - 77
52LEUPROAA87 - 14088 - 141
62LEUPROBB87 - 14088 - 141
72LEUPROCC87 - 14088 - 141
82LEUPRODD87 - 14088 - 141

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Components

#1: Protein
Regulatory protein MarR


Mass: 16498.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 89/1591 / Gene: ZP_00875883.1, SsuiDRAFT_0346 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2ZYK0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: NANODROP, 0.2M NaCl, 20.0% PEG 8000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9798
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97981
ReflectionResolution: 2.2→15.895 Å / Num. obs: 31068 / % possible obs: 95.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 37.26 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.321.90.4171.7867945740.41797.1
2.32-2.461.90.2722.8823343540.27297
2.46-2.631.90.1913.9772740780.19196.9
2.63-2.841.90.1285.9721438290.12897.3
2.84-3.111.90.0828.4659635030.08296.9
3.11-3.481.90.05611.4592231350.05696
3.48-4.021.90.04513.6517827270.04594.6
4.02-4.921.80.03518.2412922500.03591.5
4.92-6.9620.0415.3356117520.0493
6.96-15.8952.10.03512.618268720.03582.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→15.895 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.317 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.248
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 0-1 IN CHAIN A, 0-1, 78-84 IN CHAIN B, 0-1 IN CHAIN C, AND 0-1, 78-85 IN CHAIN D ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. GOL AND PO4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 6. R-FACTORS ARE SLIGHTLY HIGH, ESPECIALLY NEAR 5.5 A RESOLUTION SHELL.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1581 5.1 %RANDOM
Rwork0.223 ---
obs0.225 31066 95.45 %-
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: 39.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20.16 Å2
2---0.35 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 34 224 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224462
X-RAY DIFFRACTIONr_bond_other_d0.0020.022979
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9936056
X-RAY DIFFRACTIONr_angle_other_deg1.27537357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1315551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.68425.248202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74515846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5451529
X-RAY DIFFRACTIONr_chiral_restr0.0810.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024813
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02779
X-RAY DIFFRACTIONr_nbd_refined0.150.2957
X-RAY DIFFRACTIONr_nbd_other0.1110.22741
X-RAY DIFFRACTIONr_nbtor_refined0.1330.22090
X-RAY DIFFRACTIONr_nbtor_other0.0710.22099
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0840.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0550.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.130.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.212
X-RAY DIFFRACTIONr_mcbond_it0.97733422
X-RAY DIFFRACTIONr_mcbond_other0.19931086
X-RAY DIFFRACTIONr_mcangle_it1.28854456
X-RAY DIFFRACTIONr_scbond_it3.0781823
X-RAY DIFFRACTIONr_scangle_it4.372111594
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A749MEDIUM POSITIONAL0.310.5
2B749MEDIUM POSITIONAL0.260.5
3C749MEDIUM POSITIONAL0.320.5
4D749MEDIUM POSITIONAL0.240.5
1A801LOOSE POSITIONAL0.625
2B801LOOSE POSITIONAL0.575
3C801LOOSE POSITIONAL0.615
4D801LOOSE POSITIONAL0.595
1A749MEDIUM THERMAL0.362
2B749MEDIUM THERMAL0.252
3C749MEDIUM THERMAL0.382
4D749MEDIUM THERMAL0.352
1A801LOOSE THERMAL0.4410
2B801LOOSE THERMAL0.3310
3C801LOOSE THERMAL0.4410
4D801LOOSE THERMAL0.4210
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 143 -
Rwork0.302 2146 -
all-2289 -
obs--96.87 %
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)
12.1090.5058-0.14592.7553-1.11741.34060.04690.00480.21730.11770.06150.1718-0.0537-0.0395-0.1084-0.17940.00650.018-0.0384-0.0247-0.0988-13.30919.893-24.89
22.28991.43370.41462.93760.94173.5014-0.39970.66350.3223-0.58220.46450.2391-0.25370.1126-0.06480.0129-0.145-0.05580.15560.14070.0796-14.97731.787-46.597
30.5672-0.045-1.05020.84240.90324.2184-0.019-0.07570.0282-0.0982-0.04180.0659-0.06490.45520.0607-0.11860.0136-0.05630.09660.0157-0.08318.12210.005-55.562
43.6350.22321.91431.1637-0.20612.09480.1823-0.2707-0.49360.0447-0.0302-0.06760.3396-0.2064-0.1521-0.1484-0.01890.0246-0.0131-0.00440.052313.3764.938-31.988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1413 - 142
2X-RAY DIFFRACTION2BB2 - 773 - 78
3X-RAY DIFFRACTION2BB85 - 14186 - 142
4X-RAY DIFFRACTION3CC2 - 1413 - 142
5X-RAY DIFFRACTION4DD2 - 773 - 78
6X-RAY DIFFRACTION4DD86 - 14187 - 142

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