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- PDB-3fkq: Crystal structure of NtrC-like two-domain protein (RER07020700132... -

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Basic information

Entry
Database: PDB / ID: 3fkq
TitleCrystal structure of NtrC-like two-domain protein (RER070207001320) from Eubacterium rectale at 2.10 A resolution
ComponentsNtrC-like two-domain protein
Keywordsstructural genomics / unknown function / RER070207001320 / NtrC-like two-domain protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Ntrc-like two-domain protein. / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / NtrC-like two-domain protein
Similarity search - Component
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization.
Authors: Xu, Q. / Christen, B. / Chiu, H.J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Figurski, D.H. / Shapiro, L. / Wilson, I.A.
History
DepositionDec 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 14, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
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 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NtrC-like two-domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3639
Polymers42,6871
Non-polymers1,6768
Water2,522140
1
A: NtrC-like two-domain protein
hetero molecules

A: NtrC-like two-domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,72618
Polymers85,3742
Non-polymers3,35216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8310 Å2
ΔGint-104 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.506, 79.495, 55.022
Angle α, β, γ (deg.)90.000, 96.160, 90.000
Int Tables number5
Space group name H-MC121
DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NtrC-like two-domain protein


Mass: 42686.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Gene: RER070207001320 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: D0VX10*PLUS

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Non-polymers , 7 types, 148 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.57
Details: 2.1M ammonium sulfate, 2.25% polyethylene glycol 400, 15.0% Glycerol, 0.1M HEPES pH 7.57, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97908,0.97845
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979081
30.978451
ReflectionResolution: 2.1→29.161 Å / Num. obs: 30416 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 36.83 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.832
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.153.20.6271.2731822580.627100
2.15-2.213.20.5341.4705221790.534100
2.21-2.283.20.4291.7689421260.429100
2.28-2.353.20.3732670420670.373100
2.35-2.423.30.3182.3656220160.318100
2.42-2.513.20.2542.9621619190.254100
2.51-2.63.20.2113.4607018680.211100
2.6-2.713.20.1853.9580117910.185100
2.71-2.833.20.1544.5561817320.154100
2.83-2.973.20.1166.1535416550.116100
2.97-3.133.20.16.6510015790.1100
3.13-3.323.20.0817.8481814880.081100
3.32-3.553.20.0728.6447913840.07299.9
3.55-3.833.20.0629.8427813190.06299.8
3.83-4.23.20.05710.5391112080.05799.7
4.2-4.73.20.05111.5349210760.05199.6
4.7-5.423.20.05411.530949590.05499.5
5.42-6.643.20.0669.225858190.06699.3
6.64-9.393.20.0599.719986320.05998.9
9.39-29.163.10.04912.610423410.04995

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.161 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.899 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.15
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. ATP AND MG ARE MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGS. PEG 400 (2PE), ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. ATP AND MG ARE MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGS. PEG 400 (2PE), SULFATE (SO4), CHLORIDE(CL), AND GLYCEROL (GOL) MODELED ARE PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1535 5 %RANDOM
Rwork0.19 ---
obs0.191 30416 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.89 Å2 / Biso mean: 38.147 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20.84 Å2
2--3.46 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 79 140 2973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222891
X-RAY DIFFRACTIONr_bond_other_d0.0020.021900
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9893907
X-RAY DIFFRACTIONr_angle_other_deg0.98534696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54726.129124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71415517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.848156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_mcbond_it1.531768
X-RAY DIFFRACTIONr_mcbond_other0.3993725
X-RAY DIFFRACTIONr_mcangle_it2.66352862
X-RAY DIFFRACTIONr_scbond_it5.07781123
X-RAY DIFFRACTIONr_scangle_it7.478111041
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 104 -
Rwork0.297 2149 -
all-2253 -
obs--99.82 %
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)
14.27120.95410.39012.31660.19082.2567-0.11590.20520.1432-0.08990.12970.2298-0.0888-0.2781-0.01380.0689-0.066-0.00620.12970.0170.024128.663392.08248.1982
21.1920.2175-0.08460.50020.01851.6564-0.04980.15180.045-0.0621-0.01010.00370.10070.20730.05990.0290.01260.01860.0520.01580.02185.812960.149816.6049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 114
2X-RAY DIFFRACTION2A115 - 354

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