PDB-4k3z: Crystal structure of D-erythrulose 4-phosphate dehydrogenase from...

ID or keywords:

Entry

Database: PDB / ID: 4k3z

Title

Crystal structure of D-erythrulose 4-phosphate dehydrogenase from Brucella melitensis, solved by iodide SAD

Components

D-erythrulose 4-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / Brucella melitensis / D-erythrulose 4-phosphate dehydrogenase / iodide SAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity
Similarity search - Function

Biological species

Brucella melitensis bv. 1 (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of D-erythrulose 4-phosphate dehydrogenase from Brucella melitensis, solved by iodide SAD
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Clifton, M.C. / Lorimer, D. / Edwards, T.E.

History

Deposition	Apr 11, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Mar 13, 2024	Group: Source and taxonomy / Category: entity_src_gen

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4k3z.cif.gz	255 KB	Display	PDBx/mmCIF format
PDB format	pdb4k3z.ent.gz	206.6 KB	Display	PDB format
PDBx/mmJSON format	4k3z.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4k3z_validation.pdf.gz	459.4 KB	Display	wwPDB validaton report
Full document	4k3z_full_validation.pdf.gz	460.8 KB	Display
Data in XML	4k3z_validation.xml.gz	28.1 KB	Display
Data in CIF	4k3z_validation.cif.gz	42.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k3/4k3z ftp://data.pdbj.org/pub/pdb/validation_reports/k3/4k3z	HTTPS FTP

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Related structure data

Similar structure data	6t7e-2 1jy7-1 6kv3-2 2pzb-1 1h1m-2 2isq-1 2cb0-d 5k85-1 1h1m-1 4ry5-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BrmeA.18135.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: D-erythrulose 4-phosphate dehydrogenase

B: D-erythrulose 4-phosphate dehydrogenase

hetero molecules

75.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-erythrulose 4-phosphate dehydrogenase

hetero molecules

A: D-erythrulose 4-phosphate dehydrogenase

hetero molecules

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

2

B: D-erythrulose 4-phosphate dehydrogenase

hetero molecules

B: D-erythrulose 4-phosphate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	103.500, 103.500, 256.540
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6₂22

Components on special symmetry positions

ID	Model	Components
1	1	A-703- HOH
2	1	B-743- HOH

#1: Protein	D-erythrulose 4-phosphate dehydrogenase / EryC family protein Mass: 37344.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / Gene: BAWG_2138, BMEII0428 / Plasmid: BrmeA.18135.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8YCV0, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.66	54.4
2

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EmeraldBio JCSG screen, a3: 20% PEG 3350, 200mM ammonium citrate; BrmeA.18135.a.A1.PS01411 at 20mg/ml; crystal from tray 235328a3 incubated with 500mM NaI, 20% EG in 2 steps, pH 7.5, VAPOR ...

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Data collection

Diffraction

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

Diffraction source

Source	Type	ID	Wavelength (Å)
ROTATING ANODE	RIGAKU	1	1.5418
ROTATING ANODE	RIGAKU	2	1.5418

Detector

Type	ID	Detector	Date
RIGAKU SATURN 944+	1	CCD	Jul 6, 2012
RIGAKU SATURN 944+	2	CCD	Mar 30, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Number: 1452860 / R_merge(I) obs: 0.076 / D res high: 2.3 Å / Num. obs: 68952 / % possible obs: 99.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
2.3	2.36	5074	98.7	1	0.281
2.36	2.42	4970	99.9	1	0.26
2.42	2.49	4822	100	1	0.219
2.49	2.57	4673	100	1	0.192
2.57	2.66	4592	99.9	1	0.174
2.66	2.75	4410	100	1	0.152
2.75	2.85	4220	100	1	0.132
2.85	2.97	4103	99.9	1	0.117
2.97	3.1	3904	99.9	1	0.094
3.1	3.25	3771	100	1	0.083
3.25	3.43	3544	100	1	0.07
3.43	3.64	3382	99.9	1	0.062
3.64	3.89	3170	99.8	1	0.057
3.89	4.2	2955	100	1	0.052
4.2	4.6	2717	100	1	0.047
4.6	5.14	2460	100	1	0.045
5.14	5.94	2153	99.9	1	0.045
5.94	7.27	1839	99.9	1	0.042
7.27	10.29	1420	99.6	1	0.032

Reflection

Resolution: 1.95→50 Å / Num. all: 60098 / Num. obs: 59958 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.2 % / B_iso Wilson estimate: 22.275 Å² / R_merge(I) obs: 0.09 / R_sym value: 0.09 / Net I/σ(I): 24.13

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
1.95-2	0.257	6.65	12442	3912	1,2	97.6
2-2.06	0.167	7.54	16910	4019	1,2	94.9
2.06-2.12	0.153	10.14	22671	4103	1,2	99
2.12-2.18	0.138	13.95	31564	4013	1,2	100
2.18-2.25	0.13	17.59	40017	3925	1,2	100
2.25-2.33	0.115	19.54	39184	3750	1,2	100
2.33-2.42	0.11	20.35	38380	3661	1,2	100
2.42-2.52	0.098	22.7	36941	3546	1,2	100
2.52-2.63	0.089	24.57	35152	3360	1,2	99.9
2.63-2.76	0.084	25.78	33943	3256	1,2	99.8
2.76-2.91	0.078	27.93	31973	3079	1,2	99.8
2.91-3.08	0.067	31.91	30137	2930	1,2	99.6
3.08-3.3	0.061	35.16	28224	2765	1,2	99.4
3.3-3.56	0.054	39.29	25925	2578	1,2	99.2
3.56-3.9	0.049	42.35	23477	2387	1,2	98.9
3.9-4.36	0.046	43.38	21129	2163	1,2	98.7
4.36-5.03	0.046	44.81	18867	1923	1,2	98
5.03-6.17	0.046	41.53	16451	1643	1,2	97.3
6.17-8.72	0.042	39.9	12749	1309	1,2	96.3
8.72-50	0.028	42.49	6933	760	1,2	90.4

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Phasing

Phasing	Method: SAD
Phasing MAD	D res high: 2.3 Å / D res low: 44.59 Å / FOM : 0.331 / FOM acentric: 0.371 / FOM centric: 0.109 / Reflection: 37265 / Reflection acentric: 31621 / Reflection centric: 5599

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.2	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
JDirector		data collection
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.95→44.86 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.899 / WR_factor R_free: 0.2186 / WR_factor R_work: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8772 / SU B: 6.721 / SU ML: 0.102 / SU R Cruickshank DPI: 0.15 / SU R_free: 0.1382 / Isotropic thermal model: isotropic TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2257	3029	5.1 %	RANDOM
R_work	0.1927	-	-	-
obs	0.1944	56896	99.75 %	-
all	-	60098	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 62.19 Å² / B_iso mean: 17.7039 Å² / B_iso min: 8.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	0.25 Å²	0 Å²
2-	-	0.25 Å²	0 Å²
3-	-	-	-0.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→44.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4852	0	26	513	5391

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	5019
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4680
X-RAY DIFFRACTION	r_angle_refined_deg	1.366	1.948	6822
X-RAY DIFFRACTION	r_angle_other_deg	0.814	3	10745
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.019	5	623
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.343	23.618	246
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.032	15	798
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.551	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	740
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5732
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1176
X-RAY DIFFRACTION	r_mcbond_it	0.442	0.977	2471
X-RAY DIFFRACTION	r_mcbond_other	0.441	0.976	2470
X-RAY DIFFRACTION	r_mcangle_it	0.752	1.46	3086

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.259	205	-
R_work	0.206	4028	-
all	-	4233	-
obs	-	4333	97.56 %

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	0.3059	0.0469	-0.112	0.5823	-0.3572	0.7311	-0.0009	-0.0024	-0.0428	-0.0021	-0.0228	0.0036	0.0425	-0.0229	0.0237	0.0745	0.0328	0.0062	0.0318	-0.0039	0.0595	16.7881	30.4771	49.6477
2	0.2296	0.0379	-0.0026	1.1905	0.483	0.7731	0.0072	0.0121	0.0152	-0.0395	-0.0127	0.0343	-0.0347	-0.0024	0.0055	0.0739	0.0571	-0.0015	0.0461	0.0066	0.0514	16.0025	51.7214	46.4878
3	0.3178	0.0827	-0.1166	0.3029	-0.119	0.7155	0.0094	-0.0121	0.0053	0.0069	-0.0293	0.0515	-0.0327	-0.0568	0.0199	0.0646	0.0592	0.0034	0.0622	-0.0006	0.0659	6.3577	50.2769	56.6018
4	2.4365	-1.1974	0.7178	0.7087	0.1248	3.9149	-0.1158	-0.2728	0.0151	0.0689	0.0472	-0.0001	0.2963	-0.0727	0.0686	0.1164	0.0303	0.0353	0.1298	0.016	0.0549	4.4488	38.1406	75.3592
5	1.5182	-0.1125	-0.1699	0.5757	-0.1577	0.2983	-0.0645	-0.1718	-0.031	0.0662	0.0568	0.0568	0.0991	-0.0024	0.0077	0.0914	0.0313	0.0204	0.0515	0.0027	0.0361	14.8769	28.9939	63.658
6	0.2442	-0.1363	-0.0169	0.4194	0.0112	0.5828	0.0027	0.0337	-0.0477	-0.027	0.0109	0.0878	-0.0302	-0.0755	-0.0136	0.08	0.0291	-0.0042	0.0304	0.0002	0.0776	10.9018	38.3401	16.3945
7	2.881	0.0732	0.4505	0.4486	0.1044	0.5076	0.0364	0.0075	-0.0189	0.042	0.0101	0.0147	0.0555	-0.0125	-0.0466	0.0934	0.0361	0.0036	0.0167	0.0036	0.0448	21.9029	35.8166	19.7213
8	0.4394	0.0182	-0.198	0.433	0.1518	0.5576	-0.05	0.0165	-0.0698	-0.0474	0.0153	0.0041	0.0548	-0.0081	0.0348	0.1052	0.0317	0.0012	0.0158	-0.0015	0.065	29.8702	26.9647	13.0208
9	3.041	-0.9378	2.3607	7.0456	-0.7542	4.9165	0.1026	0.2156	0.094	-0.6259	-0.163	-0.4736	-0.0476	-0.0004	0.0604	0.1389	0.0349	0.0256	0.0817	-0.0149	0.0486	15.7867	32.4458	-7.6626
10	0.5732	-0.4636	0.1056	1.5059	0.0973	0.3978	0.0198	0.1091	-0.0891	-0.1965	-0.0343	0.1049	0.0178	-0.0392	0.0145	0.1134	0.0089	-0.0186	0.0464	-0.0301	0.0451	10.8467	31.988	1.9488

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 78
2	X-RAY DIFFRACTION	2	A	79 - 130
3	X-RAY DIFFRACTION	3	A	131 - 233
4	X-RAY DIFFRACTION	4	A	234 - 267
5	X-RAY DIFFRACTION	5	A	268 - 310
6	X-RAY DIFFRACTION	6	B	0 - 57
7	X-RAY DIFFRACTION	7	B	58 - 91
8	X-RAY DIFFRACTION	8	B	92 - 227
9	X-RAY DIFFRACTION	9	B	228 - 254
10	X-RAY DIFFRACTION	10	B	255 - 310

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