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- PDB-3fd3: Structure of the C-terminal domains of a LysR family protein from... -

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Basic information

Entry
Database: PDB / ID: 3fd3
TitleStructure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.
Componentschromosome replication initiation inhibitor protein
Keywordstranscription regulator / Agrobacterium tumefaciens / structural genomics / LysR / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
HTH-type transcriptional regulator ArgP / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...HTH-type transcriptional regulator ArgP / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, LysR family
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCuff, M.E. / Xu, X. / Zeng, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.
Authors: Cuff, M.E. / Xu, X. / Zeng, H. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 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 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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

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Assembly

Deposited unit
A: chromosome replication initiation inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2325
Polymers22,6091
Non-polymers6234
Water4,252236
1
A: chromosome replication initiation inhibitor protein
hetero molecules

A: chromosome replication initiation inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,46410
Polymers45,2182
Non-polymers1,2468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.613, 53.613, 188.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein chromosome replication initiation inhibitor protein / Transcriptional regulator / LysR family


Mass: 22609.021 Da / Num. of mol.: 1 / Fragment: residues 94-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Strain: C58 / Gene: AGR_C_1691, Atu0928, oriC / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CJQ0

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Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.6
Details: 0.1M sodium citrate pH5.6, 0.1M ammonium acetate, 15% PEG 4000, 1/800 (w/w) endoproteinase Glu-C V8, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935,0.97948
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979481
ReflectionRedundancy: 14.8 % / Av σ(I) over netI: 51 / Number: 457468 / Rmerge(I) obs: 0.074 / Χ2: 1.65 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 30842 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.615099.610.0544.99613.9
3.664.6110010.0493.17714.6
3.23.6610010.0643.09815
2.913.210010.0732.68215.3
2.72.9110010.0792.10315.6
2.542.710010.091.73115.7
2.412.5410010.0931.47915.7
2.312.4110010.1031.38215.8
2.222.3110010.1191.27915.8
2.142.2210010.1321.1715.9
2.072.1410010.1451.1115.8
2.022.0710010.1761.04815.9
1.962.0210010.2110.96715.8
1.911.9610010.2410.89516
1.871.9110010.3270.86415.7
1.831.8710010.3750.80415.3
1.791.8399.510.3730.75114.1
1.761.7995.910.4270.73712.2
1.731.7691.510.4640.76511
1.71.7378.410.4050.73510.2
ReflectionResolution: 1.7→50 Å / Num. all: 30842 / Num. obs: 30842 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 14.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.648 / Net I/σ(I): 51
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7310.20.40512350.735178.4
1.73-1.76110.46413690.765191.5
1.76-1.7912.20.42714750.737195.9
1.79-1.8314.10.37315050.751199.5
1.83-1.8715.30.37515400.8041100
1.87-1.9115.70.32715520.8641100
1.91-1.96160.24115140.8951100
1.96-2.0215.80.21115360.9671100
2.02-2.0715.90.17615511.0481100
2.07-2.1415.80.14515611.111100
2.14-2.2215.90.13215341.171100
2.22-2.3115.80.11915561.2791100
2.31-2.4115.80.10315441.3821100
2.41-2.5415.70.09315831.4791100
2.54-2.715.70.0915631.7311100
2.7-2.9115.60.07915812.1031100
2.91-3.215.30.07315902.6821100
3.2-3.66150.06416113.0981100
3.66-4.6114.60.04916503.1771100
4.61-5013.90.05417924.996199.6

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.7 Å / D res low: 50 Å / FOM : 0.359 / FOM acentric: 0.373 / FOM centric: 0.285 / Reflection: 30738 / Reflection acentric: 25847 / Reflection centric: 4891
Phasing MAD set

Highest resolution: 1.7 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.9610.10.100258474891
20.920.827.410.30.520.55244464746
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
110.99-501.7210.80.4005498
16.17-10.991.810.70.300371254
14.29-6.171.4610.50.300992396
13.29-4.291.2410.30.2001915553
12.67-3.291.6410.20.1003137692
12.24-2.672.4310.10004677833
11.93-2.244.6610.10006517993
11.7-1.9314.751000081841072
210.99-500.70.6411.914.71.861.385496
26.17-10.990.610.629.312.92.11.4371254
24.29-6.170.740.659.613.41.440.93992396
23.29-4.290.840.89.612.90.970.661915553
22.67-3.290.910.797.510.80.770.563137692
22.24-2.670.940.896.58.50.530.424676833
21.93-2.240.980.956.89.10.290.236514993
21.7-1.930.990.987.78.90.160.176787929
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se56.45636-0.674-0.772-0.0750
2Se52.91705-0.595-1.046-0.0730
3Se61.49677-0.778-0.605-0.0850
4Se43.27951-1.071-0.534-0.0390
5Se78.55586-0.44-1.121-0.0530
6Se53.371-0.769-0.617-0.0480
7Se55.88602-0.674-0.772-0.075-0.156
8Se49.81-0.595-1.046-0.073-0.119
9Se59.34161-0.777-0.607-0.085-0.16
10Se43.1117-1.071-0.534-0.039-0.114
11Se78.64132-0.439-1.12-0.053-0.113
12Se31.347-0.544-1.059-0.086-0.004
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.99-500.620.7920.5251525498
6.17-10.990.7520.8490.61625371254
4.29-6.170.7030.770.5351388992396
3.29-4.290.6380.7020.41624681915553
2.67-3.290.5770.6190.38638293137692
2.24-2.670.4490.4810.26955104677833
1.93-2.240.2680.2830.16575106517993
1.7-1.930.1340.140.083925681841072
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 30738
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.18-10040.30.868509
5.6-7.1835.60.917514
4.79-5.6400.934563
4.25-4.7933.90.952638
3.86-4.2540.40.942696
3.56-3.8639.10.932761
3.32-3.5645.60.93815
3.12-3.3242.50.923871
2.96-3.1246.20.914909
2.82-2.9647.60.902937
2.69-2.8249.90.896991
2.59-2.6950.10.8721052
2.49-2.5953.10.8671069
2.4-2.4952.10.8491105
2.33-2.457.10.8441122
2.25-2.3358.90.8441185
2.19-2.2561.50.821231
2.13-2.1967.10.7991235
2.08-2.1366.40.7881266
2.03-2.0868.70.7471309
1.98-2.0370.20.7421326
1.93-1.98740.7461373
1.89-1.9373.90.721384
1.85-1.8975.40.7211411
1.82-1.8578.10.6911455
1.78-1.8278.60.7251448
1.75-1.7881.10.7011414
1.7-1.7582.90.6572149

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.7→37.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.123 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1550 5 %RANDOM
Rwork0.169 ---
all0.171 30737 --
obs0.171 30737 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.77 Å2 / Biso mean: 26.747 Å2 / Biso min: 17.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 40 236 1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221819
X-RAY DIFFRACTIONr_bond_other_d0.0010.021225
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9762494
X-RAY DIFFRACTIONr_angle_other_deg0.8313.0052911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18822.33877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79315274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6291518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212097
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
X-RAY DIFFRACTIONr_mcbond_it0.761.51131
X-RAY DIFFRACTIONr_mcbond_other0.2181.5453
X-RAY DIFFRACTIONr_mcangle_it1.38921839
X-RAY DIFFRACTIONr_scbond_it2.2343688
X-RAY DIFFRACTIONr_scangle_it3.5034.5654
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 80 -
Rwork0.274 1767 -
all-1847 -
obs--81.69 %
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)
11.1326-0.34230.50691.2435-0.17482.40990.0175-0.05350.05660.011-0.0382-0.0827-0.05320.14460.02070.0148-0.0112-0.0070.07090.00260.010625.223814.83515.9164
21.20120.10660.48361.69130.65563.48010.04520.0673-0.08090.06050.0608-0.16690.41520.2653-0.10610.10470.0654-0.01960.0424-0.01670.022324.51793.3905-8.8982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 184
2X-RAY DIFFRACTION1A286 - 318
3X-RAY DIFFRACTION2A185 - 285

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