PDB-5cdh: Structure of Legionella pneumophila Histidine Acid Phosphatase co...

ID or keywords:

Entry

Database: PDB / ID: 5cdh

Title

Structure of Legionella pneumophila Histidine Acid Phosphatase complexed with L(+)-tartrate

Components

Major acid phosphatase

Keywords

HYDROLASE/HYDROLASE Inhibitor / HISTIDINE ACID PHOSPHATASE / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex

Function / homology

Function and homology information

Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Legionella pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.001 Å

Authors

Tanner, J.J.

Citation

Journal: Arch.Biochem.Biophys. / Year: 2015
Title: Crystal structure and tartrate inhibition of Legionella pneumophila histidine acid phosphatase.
Authors: Dhatwalia, R. / Singh, H. / Reilly, T.J. / Tanner, J.J.

History

Deposition	Jul 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5cdh.cif.gz	1001.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5cdh.ent.gz	835.3 KB	Display	PDB format
PDBx/mmJSON format	5cdh.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5cdh_validation.pdf.gz	496.6 KB	Display	wwPDB validaton report
Full document	5cdh_full_validation.pdf.gz	510.3 KB	Display
Data in XML	5cdh_validation.xml.gz	92.7 KB	Display
Data in CIF	5cdh_validation.cif.gz	126.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cd/5cdh ftp://data.pdbj.org/pub/pdb/validation_reports/cd/5cdh	HTTPS FTP

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Related structure data

Related structure data	3it1S S: Starting model for refinement
Similar structure data	3o1q-d 5nps-d 4n39-d 1k75-d 3it0-d 6u9j-d 3it2-d 7814 6ma2-d 6ma5-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

3it1S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#225 - Sep 2018 Phytase similarity (5) #257 - May 2021 Fetal Hemoglobin similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Major acid phosphatase

B: Major acid phosphatase

C: Major acid phosphatase

D: Major acid phosphatase

E: Major acid phosphatase

F: Major acid phosphatase

G: Major acid phosphatase

H: Major acid phosphatase

hetero molecules

308 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Major acid phosphatase

B: Major acid phosphatase

hetero molecules

defined by author&software
77.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Major acid phosphatase

D: Major acid phosphatase

hetero molecules

defined by author&software
76.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Major acid phosphatase

F: Major acid phosphatase

hetero molecules

defined by author&software
77.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Major acid phosphatase

H: Major acid phosphatase

hetero molecules

defined by author&software
76.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	217.889, 134.274, 135.780
Angle α, β, γ (deg.)	90.000, 127.460, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	F-628- HOH

#1: Protein	Major acid phosphatase Mass: 37982.008 Da / Num. of mol.: 8 / Fragment: UNP residues 27-352 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: map / Production host: Escherichia coli (E. coli) / References: UniProt: Q9APF7
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 660 / 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	Density Matthews: 2.59 Å³/Da / Density % sol: 52.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 and 0.2 M sodium acetate / PH range: 4.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97903 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97903 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 207120 / % possible obs: 99.6 % / Redundancy: 3.6 % / B_iso Wilson estimate: 24.48 Å² / R_merge(I) obs: 0.079 / Χ²: 1.5 / Net I/av σ(I): 20.286 / Net I/σ(I): 10.2 / Num. measured all: 745974

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2-2.07	3.3	0.451	20419	0.918	98.6
2.07-2.15	3.4	0.335	20504	0.934	98.8
2.15-2.25	3.5	0.263	20552	0.977	99.2
2.25-2.37	3.5	0.2	20655	1.018	99.5
2.37-2.52	3.6	0.158	20729	1.052	99.8
2.52-2.71	3.7	0.121	20766	1.196	100
2.71-2.99	3.8	0.089	20790	1.407	100
2.99-3.42	3.8	0.067	20815	1.955	100
3.42-4.31	3.7	0.054	20851	2.835	99.9
4.31-50	3.6	0.04	21039	2.483	99.9

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.15	data extraction
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3IT1

3it1

Resolution: 2.001→42.882 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2239	10417	5.03 %
R_work	0.1865	196615	-
obs	0.1884	207032	99.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 120.59 Å² / B_iso mean: 31.9069 Å² / B_iso min: 10.87 Å²

Refinement step

Cycle: final / Resolution: 2.001→42.882 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20170	0	261	660	21091
B_iso mean	-	-	44.63	27.91	-
Num. residues	-	-	-	-	2605

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	20973
X-RAY DIFFRACTION	f_angle_d	0.971	28558
X-RAY DIFFRACTION	f_chiral_restr	0.04	3207
X-RAY DIFFRACTION	f_plane_restr	0.004	3671
X-RAY DIFFRACTION	f_dihedral_angle_d	14.037	7599

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0009-2.0237	0.2932	343	0.2318	6079	6422	93
2.0237-2.0475	0.2779	336	0.2296	6435	6771	98
2.0475-2.0725	0.2704	355	0.2283	6533	6888	99
2.0725-2.0987	0.2635	334	0.2177	6528	6862	99
2.0987-2.1263	0.2716	335	0.214	6484	6819	99
2.1263-2.1554	0.2519	323	0.2019	6506	6829	99
2.1554-2.1862	0.2391	327	0.2029	6522	6849	99
2.1862-2.2189	0.2478	359	0.2025	6528	6887	99
2.2189-2.2535	0.264	326	0.2077	6523	6849	99
2.2535-2.2905	0.2803	337	0.1966	6554	6891	99
2.2905-2.33	0.2532	368	0.1924	6567	6935	100
2.33-2.3723	0.2331	353	0.1913	6545	6898	100
2.3723-2.418	0.2575	351	0.1972	6549	6900	100
2.418-2.4673	0.2595	362	0.1954	6542	6904	100
2.4673-2.5209	0.2258	351	0.1892	6555	6906	100
2.5209-2.5796	0.2398	304	0.191	6655	6959	100
2.5796-2.6441	0.2509	354	0.1981	6580	6934	100
2.6441-2.7156	0.2648	365	0.2031	6554	6919	100
2.7156-2.7955	0.234	367	0.2037	6559	6926	100
2.7955-2.8857	0.271	376	0.2095	6581	6957	100
2.8857-2.9888	0.2721	353	0.2171	6585	6938	100
2.9888-3.1084	0.268	352	0.2239	6593	6945	100
3.1084-3.2498	0.2681	345	0.2174	6586	6931	100
3.2498-3.4211	0.2617	368	0.2144	6619	6987	100
3.4211-3.6353	0.2045	358	0.1876	6601	6959	100
3.6353-3.9159	0.1766	330	0.1632	6605	6935	100
3.9159-4.3096	0.1637	332	0.1496	6647	6979	100
4.3096-4.9324	0.1635	352	0.1401	6622	6974	100
4.9324-6.2113	0.1774	343	0.1573	6677	7020	100
6.2113-42.8921	0.1553	358	0.1458	6701	7059	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.414	-0.3625	0.0129	1.1293	-0.0977	0.3721	-0.0372	-0.0553	0.0011	0.0856	0.033	-0.05	0.0294	-0.1105	0.0055	0.1788	-0.0533	-0.0267	0.2436	0.0292	0.1774	123.012	27.4238	26.2496
2	1.2348	0.2103	0.0397	0.7822	-0.0748	0.7232	-0.0913	0.1482	0.0047	0.0048	0.0713	0.0611	0.1236	-0.1415	0.017	0.2645	-0.1483	-0.0014	0.3103	-0.0292	0.1862	104.2779	-1.6371	26.189
3	0.2956	-0.2573	0.1378	1.2489	-0.363	0.485	0.0776	0.0176	-0.0264	-0.05	-0.0458	0.1072	0.0028	0.1852	-0.0323	0.1997	0.011	0.0152	0.4183	-0.0605	0.1858	80.6603	85.3514	-8.2953
4	0.6882	0.0147	0.4057	1.0721	0.0104	0.7545	-0.0232	0.0604	0.1195	0.0003	-0.0192	0.0684	-0.0867	0.1356	0.0373	0.2202	-0.1579	0.0299	0.4151	-0.0295	0.2342	84.7488	113.7531	10.4448
5	1.19	0.0281	-0.3128	0.5705	-0.0543	1.4068	-0.0203	0.1326	0.0156	-0.012	0.0321	-0.05	-0.0223	0.1918	-0.0036	0.1505	-0.0214	-0.0051	0.1644	-0.0028	0.1312	112.3492	67.7325	40.7913
6	1.1083	-0.2745	-0.0161	0.6131	-0.0189	0.9787	-0.0288	-0.113	0.0521	0.058	0.0183	0.0014	-0.054	-0.0047	0.0122	0.127	-0.0385	0.0058	0.1043	0.0046	0.1453	83.2805	80.0337	54.5196
7	1.5598	0.2197	-0.0305	0.8182	-0.1137	1.2141	0.0375	-0.2144	-0.1929	0.1943	-0.0396	0.0178	0.0719	-0.2185	-0.0001	0.2795	-0.0307	-0.0206	0.2609	-0.047	0.2355	65.0821	33.4083	37.4893
8	1.3379	-0.1968	-0.5645	0.2719	-0.1855	0.536	0.025	0.2116	-0.1506	-0.0028	-0.0336	0.064	-0.0204	-0.0806	0.017	0.1949	0.034	-0.0374	0.2149	-0.0925	0.2488	70.7125	45.2277	5.8041

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A	A	25 - 350
2	X-RAY DIFFRACTION	2	chain B	B	25 - 351
3	X-RAY DIFFRACTION	3	chain C	C	25 - 351
4	X-RAY DIFFRACTION	4	chain D	D	25 - 351
5	X-RAY DIFFRACTION	5	chain E	E	25 - 350
6	X-RAY DIFFRACTION	6	chain F	F	25 - 351
7	X-RAY DIFFRACTION	7	chain G	G	25 - 350
8	X-RAY DIFFRACTION	8	chain H	H	25 - 350

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