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- PDB-4lda: Crystal structure of a CheY-like protein (tadZ) from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 4lda
TitleCrystal structure of a CheY-like protein (tadZ) from Pseudomonas aeruginosa PAO1 at 2.70 A resolution
ComponentsTadZ
KeywordsTRANSCRIPTION / Response regulator receiver domain / PF00072 / CheY-like fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Pilus assembly protein TadZ, N-terminal / Pilus assembly protein TadZ N-terminal / Response regulator / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein (tadZ) from Pseudomonas aeruginosa PAO1 at 2.70 A resolution (PSI Community Target, Shapiro)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TadZ
B: TadZ
C: TadZ
D: TadZ
E: TadZ
F: TadZ
G: TadZ
H: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,92122
Polymers108,5778
Non-polymers1,34514
Water4,990277
1
A: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7643
Polymers13,5721
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7643
Polymers13,5721
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9565
Polymers13,5721
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6682
Polymers13,5721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6682
Polymers13,5721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6682
Polymers13,5721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6682
Polymers13,5721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: TadZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7643
Polymers13,5721
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.891, 86.947, 97.486
Angle α, β, γ (deg.)90.000, 107.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TadZ


Mass: 13572.071 Da / Num. of mol.: 8 / Fragment: UNP residues 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: tadZ, PA4303 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9HW97
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (1-130) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-130) 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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.010M nickel (II) chloride, 0.70M lithium sulfate, 0.1M TRIS pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979529,0.918401,0.979188
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795291
20.9184011
30.9791881
ReflectionResolution: 2.4→47.962 Å / Num. obs: 59828 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 70.075 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.462.952.1080.6113124445599.8
2.46-2.531.6080.812719429899.8
2.53-2.61.0961.212540424799.8
2.6-2.680.9641.411757403798.8
2.68-2.770.7151.811833400499.9
2.77-2.870.4772.611352382899.8
2.87-2.980.3393.510967371199.8
2.98-3.10.235.110606359399.8
3.1-3.240.1557.19976340499.5
3.24-3.390.101109508326399.5
3.39-3.580.07413.58714306597.6
3.58-3.790.059168234289797.8
3.79-4.060.04818.87570270396.7
4.06-4.380.03821.97129253698
4.38-4.80.03224.26442231196.3
4.8-5.370.03524.95887210396
5.37-6.20.03624.45202186896.8
6.2-7.590.03325.54463159297.7
7.59-10.730.02232.13557122896
10.73-47.960.02232.6193768594.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→47.962 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9361 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. SO4 ARE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 6. THE DATA ARE ANISOTROPIC WITH A NOMINAL RESOLUTION OF 2.7 A. THERE WERE AN ADDITIONAL 15794 REFLECTIONS BETWEEN 2.4 - 2.7 A INCLUDED IN THE REFINEMENT, OF WHICH 3401 REFLECTIONS (18.8% OF THE POSSIBLE REFLECTIONS IN THE SHELL) HAD I/SIGI > 2.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2887 5 %RANDOM
Rwork0.1977 ---
obs0.1991 57789 95.44 %-
Displacement parametersBiso max: 199.3 Å2 / Biso mean: 76.9595 Å2 / Biso min: 37.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.431 Å20 Å25.1912 Å2
2---1.5423 Å20 Å2
3---1.1113 Å2
Refine analyzeLuzzati coordinate error obs: 0.413 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7164 0 70 277 7511
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3427SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes172HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1106HARMONIC5
X-RAY DIFFRACTIONt_it7409HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion960SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8363SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7409HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10078HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion2.17
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2541 159 5.34 %
Rwork0.2342 2817 -
all0.2352 2976 -
obs--95.44 %
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)
14.82710.7784-0.38312.1648-0.330.8570.0428-0.36860.27410.5078-0.1560.1985-0.2181-0.05930.1133-0.05260.0393-0.0547-0.019-0.0388-0.057646.213550.542226.5722
22.47252.40240.55343.249-0.76942.76960.2113-0.07350.35840.4851-0.08020.2716-0.455-0.2355-0.1311-0.00580.02480.0284-0.1596-0.00350.002965.286642.685143.1253
30.8168-0.74160.35063.67970.75425.9193-0.06520.03040.02210.23440.0053-0.0572-0.2904-0.12110.0599-0.1485-0.0158-0.1685-0.0815-0.1211-0.001142.470819.26655.0576
45.58360.27460.17273.59231.23851.38240.0779-0.14780.0125-0.1137-0.24990.5095-0.119-0.5460.172-0.2280.084-0.01010.0078-0.04420.023121.898536.746422.4328
51.90540.64731.19313.43951.08228.65840.35910.1322-0.3935-0.0224-0.1852-0.21130.375-0.267-0.1738-0.18550.0497-0.2514-0.0763-0.01010.096753.672516.684630.0016
65.2935-1.96340.04923.6380.15983.3489-0.15760.39480.444-0.06220.2929-0.4278-0.10790.5591-0.1354-0.2249-0.0828-0.15760.08680.0105-0.101873.077556.307112.2625
73.22651.6780.47683.94032.11423.0650.0626-0.2858-0.02950.54080.0678-0.21950.23950.0673-0.1304-0.02750.0308-0.1932-0.1477-0.0151-0.004990.709954.233647.4688
86.4341-2.3174-0.00883.8954-0.55074.1607-0.03250.5335-0.5182-0.1776-0.06070.12630.19950.11770.0932-0.2949-0.0294-0.04890.0014-0.1188-0.033493.87339.362818.7308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 127}A1 - 127
2X-RAY DIFFRACTION2{B|1 - 128}B1 - 128
3X-RAY DIFFRACTION3{C|1 - 128}C1 - 128
4X-RAY DIFFRACTION4{D|2 - 121}D2 - 121
5X-RAY DIFFRACTION5{E|1 - 120}E1 - 120
6X-RAY DIFFRACTION6{F|0 - 120}F0 - 120
7X-RAY DIFFRACTION7{G|2 - 120}G2 - 120
8X-RAY DIFFRACTION8{H|1 - 127}H1 - 127

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