PDB-3k6u: M. acetivorans Molybdate-Binding Protein (ModA) in Unliganded Ope...

ID or keywords:

Entry

Database: PDB / ID: 3k6u

Title

M. acetivorans Molybdate-Binding Protein (ModA) in Unliganded Open Form

Components

Solute-binding protein MA_0280

Keywords

TRANSPORT PROTEIN / ModA / molybdate / Methanosarcina acetivorans / periplasmic binding protein / ABC transporter / ligand / metal-binding protein

Function / homology

Function and homology information

tungstate binding / molybdate ion binding / molybdate ion transport
Similarity search - Function

Biological species

Methanosarcina acetivorans (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 1.95 Å

Authors

Chan, S. / Giuroiu, I. / Chernishof, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans
Authors: Chan, S. / Giuroiu, I. / Chernishof, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J.

History

Deposition	Oct 9, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 12, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3	Apr 4, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4	Feb 21, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3k6u.cif.gz	79.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3k6u_validation.pdf.gz	425.1 KB	Display	wwPDB validaton report
Full document	3k6u_full_validation.pdf.gz	426 KB	Display
Data in XML	3k6u_validation.xml.gz	14.3 KB	Display
Data in CIF	3k6u_validation.cif.gz	20.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k6/3k6u ftp://data.pdbj.org/pub/pdb/validation_reports/k6/3k6u	HTTPS FTP

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Related structure data

Related structure data	3k6vC 3k6wC 3k6xC C: citing same article (ref.)
Similar structure data	3twk-1 6cx3-d 5wax-2 3r5z-d 3d8r-d 1gpr-1 6xvs-d 2pjd-d 6pyo-d 6h4g-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Solute-binding protein MA_0280

39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	82.179, 82.179, 104.940
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Solute-binding protein MA_0280 Mass: 39160.156 Da / Num. of mol.: 1 / Fragment: UNP residues 27 to 352 Source method: isolated from a genetically manipulated source Details: N-terminal TEV-cleavable 6xHis-tag / Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0280, MA_0280 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q8TTZ5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Solute-binding protein MA_0280

Mass: 39160.156 Da / Num. of mol.: 1 / Fragment: UNP residues 27 to 352
Source method: isolated from a genetically manipulated source
Details: N-terminal TEV-cleavable 6xHis-tag / Source: (gene. exp.)

Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0280, MA_0280 / Plasmid: pETM-11 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q8TTZ5

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.61	52.91
2
3

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
293	1	vapor diffusion, sitting drop	6.4	1.4M tri-Ammonium Citrate, p6.4, vapor diffusion, sitting drop, temperature 293K
293	2	vapor diffusion, sitting drop	6.4	1.6M tri-Ammonium Citrate, p6.4, soaked in 0.5M potassium iodide for 30 seconds, vapor diffusion, sitting drop, temperature 293K
293	3	vapor diffusion, sitting drop	6.4	1.6M tri-Ammonium Citrate, p6.4, soaked in 1M cesium chloride for 18 minutes, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1
1,2,3		1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	ALS	8.2.2		1	0.954
SYNCHROTRON	ALS	8.2.2		2	1.459
ROTATING ANODE			OTHER	3	1.542

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Nov 21, 2004
ADSC QUANTUM 315	2	CCD	Nov 21, 2004
RIGAKU RAXIS IV++	3	IMAGE PLATE	Nov 23, 2004

Radiation

ID	Protocol	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	x-ray	1
2	SINGLE WAVELENGTH	x-ray	1
3	SINGLE WAVELENGTH	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.954	1
2	1.459	1
3	1.542	1

Reflection

Av σ(I) over netI: 22.45 / Number: 195952 / R_merge(I) obs: 0.124 / Χ²: 1 / D res high: 2.7 Å / D res low: 90 Å / Num. obs: 21339 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared
5.82	90	99.7	1	0.054	0.994
4.62	5.82	100	1	0.078	1.001
4.03	4.62	100	1	0.093	0.994
3.66	4.03	100	1	0.113	0.997
3.4	3.66	100	1	0.143	1.008
3.2	3.4	100	1	0.19	1.007
3.04	3.2	100	1	0.287	1.001
2.91	3.04	99.9	1	0.363	1.008
2.8	2.91	100	1	0.493	0.995
2.7	2.8	100	1	0.588	0.995

Reflection

Resolution: 1.94→38.26 Å / Num. obs: 29447 / % possible obs: 99.9 % / Redundancy: 10.86 % / R_merge(I) obs: 0.092 / R_sym value: 0.079 / Χ²: 1.03 / Net I/σ(I): 18.6

Reflection shell

Resolution: 1.94→2.01 Å / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 10.43 / Num. unique all: 2936 / R_sym value: 0.468 / Χ²: 1.021 / % possible all: 100

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Phasing

Phasing

Method:

MIRAS

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 29027

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.42-100	51.7	0.833	503
5.96-7.42	53.6	0.834	516
5.19-5.96	53.3	0.841	525
4.66-5.19	50.7	0.854	603
4.26-4.66	56	0.835	646
3.95-4.26	57.1	0.813	713
3.7-3.95	59.1	0.79	744
3.49-3.7	62.9	0.788	823
3.32-3.49	61.7	0.765	839
3.17-3.32	68.3	0.741	896
3.03-3.17	69.6	0.755	931
2.92-3.03	69.2	0.721	979
2.81-2.92	66.9	0.696	1015
2.72-2.81	75.4	0.604	1028
2.63-2.72	89.9	0.486	1090
2.55-2.63	90.2	0.489	1120
2.48-2.55	87.8	0.538	1135
2.42-2.48	89.3	0.548	1187
2.35-2.42	91	0.555	1214
2.3-2.35	88.8	0.542	1248
2.25-2.3	90	0.547	1272
2.2-2.25	89.3	0.498	1308
2.15-2.2	88.8	0.559	1282
2.11-2.15	88.2	0.551	1372
2.07-2.11	90.7	0.56	1401
2.03-2.07	93	0.528	1404
1.99-2.03	88.1	0.541	1413
1.95-1.99	89.8	0.501	1820

Phasing MIR

Resolution: 1.95→20 Å / FOM: 0.368 / FOM acentric: 0.363 / FOM centric: 0.513 / Reflection: 10848 / Reflection acentric: 10438 / Reflection centric: 410

Phasing MIR der

Der set-ID: 1

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.95-20	0.83	0.84	59	83.7	1.22	0.89	10438	410
2	1.95-20	0.98	0.98	71.8	93.1	0.25	0.22	7253	319
iodide
Cesium

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
9.27	20	iodide	0.85	1.29	68	112.6	2.27	1.21	239	32
6.03	9.27	iodide	0.74	0.97	53.4	93	2.39	1.34	673	48
4.47	6.03	iodide	0.77	0.71	59.8	81.1	1.75	1.07	1379	69
3.55	4.47	iodide	0.84	0.82	76.5	97.6	1.03	0.74	2313	84
2.95	3.55	iodide	0.84	0.79	58.4	78.8	0.97	0.66	3508	111
2.52	2.95	iodide	0.85	0.83	42.8	56.2	1.02	0.68	2326	66
2.2	2.52	iodide	0	0	0	0	0	0	0	0
1.95	2.2	iodide	0	0	0	0	0	0	0	0
9.27	20	Cesium	0.92	0.93	69.1	91.1	0.73	0.46	239	30
6.03	9.27	Cesium	0.9	0.91	46.2	70.4	0.82	0.46	673	48
4.47	6.03	Cesium	0.97	0.97	62.6	85.8	0.41	0.28	1379	69
3.55	4.47	Cesium	0.99	1.01	83.9	100.7	0.18	0.15	2313	84
2.95	3.55	Cesium	1	0.99	72.7	104.6	0.12	0.09	2649	88
2.52	2.95	Cesium	0	0	0	0	0	0	0	0
2.2	2.52	Cesium	0	0	0	0	0	0	0	0
1.95	2.2	Cesium	0	0	0	0	0	0	0	0

Phasing MIR der site

ID	Der-ID	B_iso (Å)	Atom type symbol	Fract x	Fract y	Fract z	Occupancy
1	iodide	25.663	I-	0.498	0.13	0.021	0.71
2	iodide	38.498	I-	0.286	0.339	0.095	0.542
3	iodide	41.684	I-	0.297	0.534	0.099	0.542
4	iodide	42.947	I-	0.186	0.16	0.144	0.518
5	iodide	42.946	I-	0.926	0.543	0.051	0.507
6	iodide	45.642	I-	0.041	0.537	0.026	0.451
7	Cesium	76.553	Cs	0.079	0.243	0.226	0.412
8	Cesium	64.82	Cs	0.655	0.595	0.048	0.25

Phasing MIR shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
9.27-20	0.613	0.605	0.673	271	239	32
6.03-9.27	0.622	0.618	0.679	721	673	48
4.47-6.03	0.511	0.505	0.617	1448	1379	69
3.55-4.47	0.354	0.35	0.479	2397	2313	84
2.95-3.55	0.309	0.305	0.44	3619	3508	111
2.52-2.95	0.283	0.28	0.369	2392	2326	66
2.2-2.52	0	0	0		0	0
1.95-2.2	0	0	0		0	0

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
CrystalClear		data collection

Refinement

Method to determine structure:

MIRAS / Resolution: 1.95→38.26 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.947 / WR_factor R_free: 0.234 / WR_factor R_work: 0.197 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.87 / SU B: 6.561 / SU ML: 0.086 / SU R Cruickshank DPI: 0.136 / SU R_free: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.208	1453	5 %	RANDOM
R_work	0.177	-	-	-
obs	0.178	29271	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 54.9 Å² / B_iso mean: 17.613 Å² / B_iso min: 5.61 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.93 Å²	0.46 Å²	0 Å²
2-	-	0.93 Å²	0 Å²
3-	-	-	-1.39 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→38.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2423	0	0	176	2599

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2493
X-RAY DIFFRACTION	r_angle_refined_deg	1.392	1.967	3401
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.982	5	313
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.176	26	125
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.497	15	403
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.826	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	381
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1941
X-RAY DIFFRACTION	r_mcbond_it	0.883	1.5	1561
X-RAY DIFFRACTION	r_mcangle_it	1.64	2	2528
X-RAY DIFFRACTION	r_scbond_it	2.613	3	932
X-RAY DIFFRACTION	r_scangle_it	4.318	4.5	872

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.267	106	-
R_work	0.211	2031	-
all	-	2137	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Origin x: 15.8757 Å / Origin y: 25.8208 Å / Origin z: 14.2498 Å

	11	12	13	21	22	23	31	32	33
T	0.0437 Å²	0.0162 Å²	-0.0005 Å²	-	0.023 Å²	-0.0007 Å²	-	-	0.0637 Å²
L	1.4481 °²	-0.2859 °²	-1.8669 °²	-	0.5945 °²	0.1416 °²	-	-	3.363 °²
S	-0.0637 Å °	-0.0434 Å °	-0.0352 Å °	0.0472 Å °	0.0116 Å °	0.0301 Å °	0.2449 Å °	0.0923 Å °	0.0521 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 201
2	X-RAY DIFFRACTION	1	A	203 - 354

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