PDB-7l2a: Molybdopterin cofactor biosynthesis protein E from Burkholderia m...

ID or keywords:

Entry

Database: PDB / ID: 7l2a

Title

Molybdopterin cofactor biosynthesis protein E from Burkholderia multivorans ATCC 17616

Components

MPT synthase subunit 2

Keywords

BIOSYNTHETIC PROTEIN / SSGCID / Molybdenum cofactor biosynthesis protein E / moaE / MPT synthase subunit 2 / molybdopterin biosynthesis / Burkholderia multivorans / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

molybdopterin synthase / molybdopterin synthase activity / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Mo-molybdopterin cofactor biosynthetic process / IMIDAZOLE / MPT synthase subunit 2

Function and homology information

Biological species

Burkholderia multivorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Molybdopterin cofactor biosynthesis protein E from Burkholderia multivorans ATCC 17616
Authors: Calhoun, B. / Weiss, M.J. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 16, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7l2a.cif.gz	162.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7l2a.ent.gz	105.6 KB	Display	PDB format
PDBx/mmJSON format	7l2a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7l2a_validation.pdf.gz	469.9 KB	Display	wwPDB validaton report
Full document	7l2a_full_validation.pdf.gz	471.6 KB	Display
Data in XML	7l2a_validation.xml.gz	14.6 KB	Display
Data in CIF	7l2a_validation.cif.gz	20.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l2/7l2a ftp://data.pdbj.org/pub/pdb/validation_reports/l2/7l2a	HTTPS FTP

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Related structure data

Related structure data	2qieS S: Starting model for refinement
Similar structure data	2ywp-d 1po9-2 2e9v-1 2ghg-d 2y05-1 1pok-1 3jvr-d 2j30-d 2e9n-d 2w98-2 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
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: MPT synthase subunit 2

B: MPT synthase subunit 2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	47.730, 72.660, 105.770
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 0 through 13 or resid 15...
d_2	ens_1	(chain "B" and ((resid 0 and (name N or name...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	HIS	LEU	A	1 - 14
d_1	2	ens_1	ALA	LEU	A	16 - 21
d_1	3	ens_1	ALA	ALA	A	23
d_1	4	ens_1	ASN	ALA	A	25 - 32
d_1	5	ens_1	PHE	PHE	A	34
d_1	6	ens_1	GLY	GLY	A	36 - 51
d_1	7	ens_1	THR	THR	A	53 - 123
d_1	8	ens_1	GLU	SER	A	126 - 133
d_1	9	ens_1	ALA	TRP	A	138 - 142
d_1	10	ens_1	DMS	DMS	D
d_2	1	ens_1	HIS	LEU	E	5 - 18
d_2	2	ens_1	ALA	LEU	E	20 - 25
d_2	3	ens_1	ALA	ALA	E	27
d_2	4	ens_1	ASN	ALA	E	29 - 36
d_2	5	ens_1	PHE	PHE	E	38
d_2	6	ens_1	GLY	ASN	E	40 - 46
d_2	7	ens_1	ALA	GLY	E	53 - 61
d_2	8	ens_1	THR	TRP	E	63 - 146
d_2	9	ens_1	DMS	DMS	G

NCS oper: (Code: givenMatrix: (-0.389527346283, 0.735325382773, 0.554585455947), (0.725574269799, -0.125881548186, 0.676532197927), (0.567283373195, 0.665920728973, -0.484498872259)Vector: 52. ...

#1: Protein	MPT synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / ...Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / Molybdopterin-converting factor large subunit / Molybdopterin-converting factor subunit 2 Mass: 18410.807 Da / Num. of mol.: 2 / Fragment: BumuA.00098.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria) Strain: ATCC 17616 / 249 / Gene: moaE, BMULJ_01820 / Plasmid: BumuA.00098.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3KFN7, molybdopterin synthase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.49 Å³/Da / Density % sol: 50.7 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Molecular Dimensions Morpheus screen, E3: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol, 0.1 M ...Details: Molecular Dimensions Morpheus screen, E3: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol, 0.1 M MES/imidazole pH 6.5: BumuA.00098.a.B1.PS37859 at 41.7mg/ml + 0.5% beta-octyl-glucoside: cryo: direct: tray 317330e3, puck xxu3-3.

Crystal

Density Matthews: 2.49 Å³/Da / Density % sol: 50.7 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen, E3: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol, 0.1 M ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2020 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.85→50 Å / Num. obs: 32130 / % possible obs: 99.9 % / Redundancy: 6.821 % / B_iso Wilson estimate: 39.047 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.042 / R_rim(I) all: 0.045 / Χ²: 0.942 / Net I/σ(I): 23.12

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
1.85-1.9	4.241	0.407	2.88	2319	0.946	0.465	99.5
1.9-1.95	5.155	0.327	4.06	2259	0.971	0.364	100
1.95-2.01	6.541	0.268	5.8	2237	0.985	0.291	100
2.01-2.07	7.336	0.212	7.96	2181	0.992	0.228	100
2.07-2.14	7.359	0.165	9.95	2070	0.994	0.177	100
2.14-2.21	7.355	0.126	13.04	2029	0.997	0.135	100
2.21-2.29	7.341	0.098	15.8	1960	0.997	0.105	100
2.29-2.39	7.347	0.085	17.84	1889	0.998	0.091	100
2.39-2.49	7.335	0.072	21.26	1820	0.999	0.077	100
2.49-2.62	7.329	0.06	25.48	1736	0.999	0.064	100
2.62-2.76	7.308	0.053	28.84	1652	0.999	0.057	100
2.76-2.93	7.296	0.045	34.36	1576	0.999	0.048	100
2.93-3.13	7.262	0.039	39.17	1495	0.999	0.042	100
3.13-3.38	7.203	0.035	44.06	1382	0.999	0.038	100
3.38-3.7	7.142	0.033	48.66	1288	0.999	0.036	100
3.7-4.14	7.074	0.032	50.31	1178	0.999	0.034	100
4.14-4.78	7.022	0.03	52.89	1041	0.999	0.033	100
4.78-5.85	6.937	0.03	52.15	885	0.999	0.033	100
5.85-8.27	6.698	0.028	51.66	711	0.999	0.031	100
8.27-50	5.78	0.032	49.55	422	0.998	0.035	98.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19rc4	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2QIE as per MoRDa

2qie

Resolution: 1.85→42.76 Å / SU ML: 0.1952 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2232	2018	6.29 %	0
R_work	0.1887	30086	-	-
obs	0.191	32104	99.86 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 45.93 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→42.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2219	0	21	178	2418

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0078	2330
X-RAY DIFFRACTION	f_angle_d	0.9393	3173
X-RAY DIFFRACTION	f_chiral_restr	0.0641	357
X-RAY DIFFRACTION	f_plane_restr	0.0091	414
X-RAY DIFFRACTION	f_dihedral_angle_d	12.0241	822

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 1.82817564282 Å

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 (%)
1.85-1.9	0.3221	130	0.2938	2095	X-RAY DIFFRACTION	99.29
1.9-1.95	0.2997	127	0.2573	2113	X-RAY DIFFRACTION	99.78
1.95-2	0.3036	135	0.26	2139	X-RAY DIFFRACTION	99.69
2-2.07	0.2919	137	0.2103	2153	X-RAY DIFFRACTION	99.83
2.07-2.14	0.2242	132	0.1876	2097	X-RAY DIFFRACTION	99.91
2.14-2.23	0.2023	112	0.1806	2155	X-RAY DIFFRACTION	99.96
2.23-2.33	0.2141	149	0.1897	2124	X-RAY DIFFRACTION	100
2.33-2.45	0.2483	158	0.1941	2120	X-RAY DIFFRACTION	100
2.45-2.61	0.2113	151	0.2026	2132	X-RAY DIFFRACTION	99.96
2.61-2.81	0.2526	147	0.1993	2166	X-RAY DIFFRACTION	99.91
2.81-3.09	0.2399	154	0.1981	2133	X-RAY DIFFRACTION	100
3.09-3.54	0.212	152	0.1903	2164	X-RAY DIFFRACTION	100
3.54-4.46	0.1976	154	0.1665	2204	X-RAY DIFFRACTION	100
4.46-42.76	0.2127	180	0.173	2291	X-RAY DIFFRACTION	99.76

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	2.78940595794	1.16310976301	-1.64262980286	1.97356759602	-1.22314369106	7.57455893161	0.0505132269809	0.435687769739	0.0877479073422	-0.223459516535	-0.0107106187553	0.395853910515	-0.175431929613	-0.768568122416	-0.031131673764	0.297233817477	0.0206060793556	-0.0560412669517	0.310577450437	-0.0428367278915	0.282107698261	11.1873582129	-4.74662884281	-35.4128319747
2	3.43230133242	0.582329517292	-0.929879558299	3.78051537895	-0.460976906922	4.3161509856	0.0224525972515	-0.164288096184	-0.125349912291	0.508671351855	-0.0390716684944	0.516091539578	0.202041471812	-0.314338370001	-0.00401395168472	0.317693529504	-0.00893885502508	0.0128177228006	0.290618944263	-0.0509010829557	0.242954305898	9.37266109156	-3.56257663357	-20.6443630014
3	3.12513124834	1.26801383705	-1.6954238775	3.81226849039	-0.917997195552	4.24451395609	-0.0110081206399	-0.0217444981468	-0.0431991892177	0.275532299178	-0.0262391839429	0.145926887057	-0.122049451995	-0.245843686157	0.0612081113713	0.291052630193	0.00751324832166	-0.0129905856441	0.242346062002	-0.0231934306966	0.252108839271	14.3393025234	-3.58528596673	-25.4193038116
4	6.07140215881	2.64669569969	-2.09538260175	8.43765091711	0.464279151049	6.53557636446	-0.378759136591	-0.259822351423	-1.45082997166	0.386804344127	-0.402107795099	-1.17767706027	1.71967304959	-0.820459466207	0.821959758341	0.952271155004	-0.127958790057	0.195287104749	0.559719117837	0.0452649574138	0.553591951318	5.80332742737	-13.3945955639	-5.63502592399
5	3.12358986504	3.17078337127	-3.95753756944	3.18346502834	-3.95760821689	4.96335970089	0.264980969939	-0.714511207798	-0.398504024978	1.13929410914	-0.286441698517	-0.743743746628	-0.379959985173	0.362832641245	0.192166063766	0.582360151878	-0.0283727751849	-0.0783230292842	0.483608393689	-0.00862899222519	0.403446422605	20.2891442595	4.0260788777	-14.5315264336
6	1.22020651528	-1.12615159883	-0.269643005805	1.49311585347	0.248968513726	0.0567753092571	0.353147356573	0.655901985407	-0.220889605327	-2.00680285339	-0.500837082693	1.22534907508	-1.28430042819	-0.860376898773	0.207710946357	1.25828823312	0.250770263493	0.0800190413005	0.668183010981	0.0249191336325	0.692449525156	32.2116515796	-27.4825186504	-42.5532556895
7	3.56961606068	0.162253076851	0.522866487845	5.09232493011	-3.70534860087	3.10138528754	0.00668614886744	0.404919836859	-0.309767413138	-0.577430039692	0.0121526604017	0.0345239588588	0.692595132153	0.096380865989	-0.0488291572377	0.463689007167	-0.00375607505517	-0.0267783598169	0.281314323696	-0.0438036230477	0.293664257819	23.3891326293	-16.0568888936	-40.2745761208
8	0.934052782992	-1.25441639206	1.59533956115	4.93360015177	-3.2654285421	7.18888949331	-0.0314498285907	0.187879217971	0.00914872471862	-0.0861764103129	-0.0878895546232	0.0346129739266	-0.602912824496	0.0459280474432	0.0874757709494	0.294852314817	-0.0214554816745	-0.0246640646849	0.287561487433	-0.00641337033439	0.260541058598	21.8346198129	-5.98042420606	-42.1886048957
9	5.91823670533	-4.91286242961	1.78932666872	4.05025795305	-1.23951588361	4.31197495146	0.540734132	1.45120213565	0.436389708667	-1.1172361486	-0.82234313622	-1.25402639461	0.635442811843	1.66371217658	0.243961477727	0.637023006102	0.139635315564	0.204157002857	0.769601534071	0.119691015914	0.604124560227	36.1025861422	-8.34448853009	-52.6771820268
10	7.20839999437	-3.78848501099	-0.241840463271	6.30366494995	-1.27450239313	2.64763581134	0.110933913981	-0.0892138248492	0.293254350318	-0.103796859335	-0.209567613106	-0.962653426203	0.495184352732	2.25173437992	-0.0623864967082	0.264131228489	0.0127302166475	-0.00336950136851	0.510146669137	0.0499147666098	0.520753873972	39.9284721732	-10.883076466	-36.6353508727
11	1.83544553785	-0.453302160066	0.887071977526	3.19995991247	-0.697277307778	8.3187264747	0.0497890461498	0.0808077246668	0.0948325520987	-0.0361152357988	-0.0306826737961	-0.226539994415	0.168482992593	0.455811890931	-0.00967251025568	0.199993124817	-0.00339712482788	-0.0200302399036	0.241430030762	-0.0110181668336	0.293451961444	28.850074872	-7.02180848173	-36.8570666436
12	7.51509079758	0.114143376495	0.223537137872	2.87636570081	1.35876834741	6.50559503729	0.121820276216	1.425602719	1.46795194806	-1.02017585864	-0.177121708387	-0.176796574975	-0.201275863594	1.84598688359	0.291578537787	0.528042011464	0.0148719913967	0.0755859758117	0.943770037713	0.277094165116	0.659506303688	36.6664884973	-1.80753081039	-53.6237093687
13	6.68217149117	1.17115063645	0.449202064888	3.03088337744	-2.12825022037	6.98658764645	-0.232832612165	0.647564872436	1.07858938239	0.0354804766354	-0.195203022857	-0.545902314249	-0.700943308554	1.83825762936	0.296375333986	0.447164510324	-0.0114184818267	0.0476422514661	0.638376733	0.0965444176349	0.788831037554	38.2415967062	1.51067464568	-42.6188259807

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 0 through 36 )	A	A	0 - 36	1 - 37
2	2	chain 'A' and (resid 37 through 72 )	A	A	37 - 72	38 - 67
3	3	chain 'A' and (resid 73 through 127 )	A	A	73 - 127	68 - 122
4	4	chain 'A' and (resid 128 through 137 )	A	A	128 - 137	123 - 130
5	5	chain 'A' and (resid 138 through 153 )	A	A	138 - 153	131 - 146
6	6	chain 'B' and (resid -4 through 3 )	B	E	-4 - 3	1 - 8
7	7	chain 'B' and (resid 4 through 22 )	B	E	4 - 22	9 - 27
8	8	chain 'B' and (resid 23 through 48 )	B	E	23 - 48	28 - 53
9	9	chain 'B' and (resid 49 through 56 )	B	E	49 - 56	54 - 61
10	10	chain 'B' and (resid 57 through 72 )	B	E	57 - 72	62 - 77
11	11	chain 'B' and (resid 73 through 120 )	B	E	73 - 120	78 - 125
12	12	chain 'B' and (resid 121 through 134 )	B	E	121 - 134	126 - 135
13	13	chain 'B' and (resid 135 through 149 )	B	E	135 - 149	136 - 146

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