PDB-6w04: Crystal structure of HAD hydrolase, family IA, variant 3 from Ent...

ID or keywords:

Entry

Database: PDB / ID: 6w04

Title

Crystal structure of HAD hydrolase, family IA, variant 3 from Entamoeba histolytica HM-1:IMSS

Components

HAD hydrolase, family IA, variant 3

Keywords

HYDROLASE / SSGCID /

Entamoeba histolytica / HAD hydrolase / family IA /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily /

hydrolase activity / HAD hydrolase, family IA, variant 3

Function and homology information

Biological species

Entamoeba histolytica (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of HAD hydrolase, family IA, variant 3 from Entamoeba histolytica HM-1:IMSS
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Feb 29, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6w04.cif.gz	131.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6w04.ent.gz	84.4 KB	Display	PDB format
PDBx/mmJSON format	6w04.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w0/6w04 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/6w04	HTTPS FTP

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Related structure data

Similar structure data	3qu7-1 3f4s-d 4aly-2 2dps-1 6rxr-2 1woj-d 4cp1-d 6rxr-3 1omv-d 2c06-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: EnhiA.01283.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (4)

Deposited unit

A: HAD hydrolase, family IA, variant 3

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	100.910, 100.910, 45.240
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: -x,-y,z+1/2

#1: Protein	HAD hydrolase, family IA, variant 3 Mass: 26373.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_073350 / Plasmid: EnhiA.01283.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C4LXK0, Hydrolases
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.3 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 24.5 mg/mL EnhiA.01283.a.AE1.PS38608 (labeled as BrabA.17285.c.AE2) in 3 mM magnesium chloride against MCSG1_A2-C2 optimization screen, condition g3 (200 mM ammonium sulfate, 26% w/v ...Details: 24.5 mg/mL EnhiA.01283.a.AE1.PS38608 (labeled as BrabA.17285.c.AE2) in 3 mM magnesium chloride against MCSG1_A2-C2 optimization screen, condition g3 (200 mM ammonium sulfate, 26% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.4), cryoprotectant: 15% ethylene glycol + 3 mM magnesium chloride in two steps, tray: 314701g3, puck wrw2-2, for experimental phasing, a crystal from MCSG1_A2-C2 optimization screen, condition e7 (300 mM lithium sulfate, 24% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.0) was soaked for 20 seconds in 90% reservoir + 10% 5 M sodium iodide in ethylene glycol, followed by another 20-second soak in 80% reservoir + 20% 5 M sodium iodide in ethylene glycol, vitrified in liquid nitrogen, tray 314703e7, puck ynn3-8

Crystal

Density Matthews: 2.52 Å³/Da / Density % sol: 51.3 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24.5 mg/mL EnhiA.01283.a.AE1.PS38608 (labeled as BrabA.17285.c.AE2) in 3 mM magnesium chloride against MCSG1_A2-C2 optimization screen, condition g3 (200 mM ammonium sulfate, 26% w/v ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Feb 5, 2020
RIGAKU SATURN 944+	2	CCD	Feb 4, 2020

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	diamond(111)	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.95→50 Å / Num. obs: 19394 / % possible obs: 100 % / Redundancy: 7.521 % / B_iso Wilson estimate: 40.227 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.068 / Χ²: 1.006 / Net I/σ(I): 18.53

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.95-2	7.568	0.494	3.8	1413	0.9	0.53	100
2-2.06	7.554	0.354	5.26	1409	0.952	0.38	100
2.06-2.12	7.557	0.269	6.98	1342	0.972	0.288	100
2.12-2.18	7.621	0.216	8.59	1303	0.981	0.231	100
2.18-2.25	7.541	0.176	10.51	1278	0.987	0.189	100
2.25-2.33	7.597	0.146	12.69	1219	0.992	0.156	100
2.33-2.42	7.586	0.121	14.51	1193	0.994	0.129	100
2.42-2.52	7.578	0.112	16.11	1161	0.994	0.12	100
2.52-2.63	7.564	0.093	18.72	1081	0.994	0.1	100
2.63-2.76	7.562	0.077	22.07	1060	0.996	0.083	100
2.76-2.91	7.557	0.067	24.33	999	0.997	0.072	100
2.91-3.08	7.515	0.062	27.23	943	0.997	0.066	100
3.08-3.3	7.47	0.055	30.36	897	0.997	0.059	100
3.3-3.56	7.536	0.051	33.07	840	0.997	0.055	100
3.56-3.9	7.427	0.05	33.58	757	0.998	0.054	100
3.9-4.36	7.485	0.05	35.35	705	0.998	0.053	100
4.36-5.03	7.369	0.048	35.21	626	0.997	0.052	99.8
5.03-6.17	7.393	0.049	34.49	519	0.997	0.052	99.8
6.17-8.72	7.18	0.048	34.39	410	0.998	0.052	99.8
8.72-50	6.469	0.051	34.13	239	0.996	0.055	98.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18rc1	refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.95→33.03 Å / SU ML: 0.2146 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.8296

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2107	1876	9.68 %	0
R_work	0.1579	-	-	-
obs	0.1629	19390	99.97 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 42.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→33.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1763	0	10	151	1924

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0089	1844
X-RAY DIFFRACTION	f_angle_d	0.8897	2498
X-RAY DIFFRACTION	f_chiral_restr	0.0575	284
X-RAY DIFFRACTION	f_plane_restr	0.0051	318
X-RAY DIFFRACTION	f_dihedral_angle_d	17.0766	685

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-2	0.3037	125	0.2203	1348	X-RAY DIFFRACTION	100
2-2.06	0.2536	147	0.1934	1346	X-RAY DIFFRACTION	100
2.06-2.13	0.2527	148	0.176	1316	X-RAY DIFFRACTION	100
2.13-2.2	0.2599	155	0.1796	1332	X-RAY DIFFRACTION	100
2.2-2.29	0.2049	134	0.1622	1348	X-RAY DIFFRACTION	100
2.29-2.4	0.23	155	0.1694	1332	X-RAY DIFFRACTION	100
2.4-2.52	0.2291	157	0.1655	1339	X-RAY DIFFRACTION	100
2.52-2.68	0.2059	145	0.1614	1320	X-RAY DIFFRACTION	100
2.68-2.89	0.2292	149	0.1603	1343	X-RAY DIFFRACTION	100
2.89-3.18	0.2092	143	0.168	1347	X-RAY DIFFRACTION	100
3.18-3.64	0.2266	139	0.1504	1352	X-RAY DIFFRACTION	100
3.64-4.58	0.1715	149	0.133	1378	X-RAY DIFFRACTION	99.93
4.58-33.03	0.1935	130	0.158	1413	X-RAY DIFFRACTION	99.68

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	2.56079551563	0.152937348874	-4.31369400269	4.41085809221	-1.25947856771	8.03870676315	-0.135798563015	0.281696150237	0.0620222238566	-0.0618075172017	-0.130859132249	0.725086420966	0.136067283734	-0.703519459497	0.243058947526	0.244252486594	0.0115737368088	-0.0489225528173	0.300786132286	-0.12188498749	0.367661222882	35.2702466302	-3.54935584805	-4.82561328925
2	7.82072604277	-6.5642833021	0.682217393978	7.88291660423	-1.30485523069	3.29558653824	0.112527905101	0.331501103664	0.559815823375	-0.462014186702	-0.278049957168	-0.450792641055	-0.0900387461669	0.200978726703	0.140924389505	0.306420505446	-0.020462804548	0.0223674962498	0.175108229346	0.00337057230347	0.210856732722	57.0263902905	-10.9872361682	-12.6534427626
3	6.43371341328	-0.257015375383	-3.89970215992	4.69460890536	-0.904189073249	7.41276545789	-0.179596859724	1.09068060207	-0.102192486374	-1.25415493294	0.1424066162	0.491858396186	0.733606460184	-0.957564664306	-0.00453988651162	0.490886482753	-0.0628327927456	-0.0797298765575	0.304612410641	0.0459076565245	0.260539607576	52.0502455407	-17.8877801614	-15.586937819
4	7.73010113193	-0.675725429295	-2.55798226891	6.75148422265	-0.0655908348797	6.74599098324	-0.446916919217	-0.395624984901	-0.138915137715	0.222209925558	-0.0725850586006	-0.635659131345	1.15429811405	0.0938493391219	0.227955881311	0.353755602199	0.0276980183147	-0.0212924362248	0.191793836911	0.037893173845	0.1967777041	56.5599259714	-22.509204978	-5.53349816904
5	5.83182088292	-1.48030433053	2.49019303784	2.65518631221	-4.43420452138	8.25478232094	0.00175967171794	-0.148698540849	-0.162733494741	0.614477478985	-0.0219896576596	-0.618738375298	-0.0334582596425	0.416583224309	0.00521020249954	0.356591286078	0.0296727096958	-0.0742106567181	0.215092585176	-0.0713351517257	0.240741846636	56.4927972582	-7.68277172675	-2.86304228607
6	7.1740302845	-3.24339134837	-2.56213488833	3.60366350792	1.04720889171	2.47682352381	0.0996195068616	0.200615538169	0.889934502484	-0.676344334412	-0.0485205722237	0.805065557019	-0.500560425299	-0.443606032708	-0.250591184966	0.435855078401	0.14875141445	-0.13498571337	0.349748112441	-0.0711027106245	0.541634417596	35.0815450356	5.96290060794	-7.7217785509
7	2.27269632045	-3.52339850225	1.60114711414	6.56054136282	-0.548456431955	4.96476960455	0.0650328436361	0.3048811279	-0.795729589136	0.291327313595	-0.292620143875	1.27714255196	0.0398379559798	-0.485431790736	0.224463595987	0.288406667695	-0.0156816320478	0.0605399967724	0.235123946553	-0.0994713989269	0.470652405349	34.9772789131	-1.89979421855	1.72229877646
8	7.20016949426	-0.261436468205	-1.95237727318	3.66855189314	0.0810164644229	6.69180927528	-0.0546486974246	-0.33504072738	0.581745838506	-0.0687854240114	-0.0322798080214	0.444907715955	-0.205492657196	-0.0918318148555	0.106479187996	0.298610242276	0.0248111452423	-0.0185693805002	0.203655765612	-0.105548868258	0.262819757513	43.3940259375	3.6063004062	1.80322351435
9	6.42548529279	5.84854034954	1.55952192744	7.83118425063	2.18142076029	5.61988485298	0.690392990373	-0.303309739612	-0.67607482507	1.24460759597	-0.349735828186	-0.629168642573	0.876926682061	0.0920790306351	-0.311406985345	0.493842800905	-0.013307440767	-0.0582251565446	0.316768299935	-0.0391235620078	0.348637052443	41.129842147	-12.5103779973	5.33395444928
10	3.22775777407	1.09905199822	-0.00431536160257	4.63699591427	0.818930389538	5.78596163842	0.0613202998225	0.00723102493494	0.110262259279	-0.136984868957	-0.189012251064	0.666651509736	0.149283445123	-0.474760909502	0.136364994964	0.268108149693	-0.0115000660823	-0.0744606396057	0.310797418349	-0.0865620506588	0.45021524134	30.651704465	-11.4426246084	-5.8474998182
11	6.06970121108	2.62092974589	-0.977660279974	4.06253935544	-1.92634104112	4.26515878538	-0.0984423606739	0.173484537587	0.731844439972	-0.56250846089	0.177900362692	1.4325445748	0.170027915617	-1.10373605728	-0.18239137254	0.409218062617	0.119599456415	-0.2168174555	0.727939176309	-0.0839358430939	0.888702091666	22.03023684	-2.52658027235	-9.06522972435

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 15 )	1 - 15	1 - 15
2	2	chain 'A' and (resid 16 through 31 )	16 - 31	16 - 31
3	3	chain 'A' and (resid 32 through 47 )	32 - 47	32 - 47
4	4	chain 'A' and (resid 48 through 61 )	48 - 61	48 - 61
5	5	chain 'A' and (resid 62 through 82 )	62 - 82	62 - 86
6	6	chain 'A' and (resid 83 through 100 )	83 - 100	87 - 104
7	7	chain 'A' and (resid 101 through 112 )	101 - 112	105 - 118
8	8	chain 'A' and (resid 113 through 133 )	113 - 133	119 - 139
9	9	chain 'A' and (resid 134 through 147 )	134 - 147	140 - 153
10	10	chain 'A' and (resid 148 through 208 )	148 - 208	154 - 219
11	11	chain 'A' and (resid 209 through 223 )	209 - 223	220 - 234

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