PDB-7kh2: Structure of N-citrylornithine decarboxylase bound with PLP

ID or keywords:

Entry

Database: PDB / ID: 7kh2

Title

Structure of N-citrylornithine decarboxylase bound with PLP

Components

N-citrylornithine decarboxylase

Keywords

BIOSYNTHETIC PROTEIN / LYASE / rhizoferrin / putrescine / ornithine / citrate / Francisella / Ralstonia / Legionella / siderophore / spermidine / iron / polyamine / decarboxylase

Function / homology

Function and homology information

diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate
Similarity search - Function

Biological species

Francisella novicida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.05 Å

Authors

Deng, X. / Tomchick, D. / Phillips, M. / Michael, A.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin.
Authors: Li, B. / Deng, X. / Kim, S.H. / Buhrow, L. / Tomchick, D.R. / Phillips, M.A. / Michael, A.J.

History

Deposition	Oct 19, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 30, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jul 28, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7kh2.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7kh2.ent.gz	846.5 KB	Display	PDB format
PDBx/mmJSON format	7kh2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7kh2_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	7kh2_full_validation.pdf.gz	1.6 MB	Display
Data in XML	7kh2_validation.xml.gz	64 KB	Display
Data in CIF	7kh2_validation.cif.gz	90.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kh/7kh2 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/7kh2	HTTPS FTP

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Related structure data

Similar structure data	4i0f-2 1tuf-d 2plj-d 6zyv-d 3zug-d 4c9b-d 3vqr-d 5bnd-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) 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: N-citrylornithine decarboxylase

B: N-citrylornithine decarboxylase

C: N-citrylornithine decarboxylase

D: N-citrylornithine decarboxylase

hetero molecules

202 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-citrylornithine decarboxylase

C: N-citrylornithine decarboxylase

hetero molecules

defined by author&software
Evidence: gel filtration
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N-citrylornithine decarboxylase

D: N-citrylornithine decarboxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.839, 279.061, 108.625
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	N-citrylornithine decarboxylase Mass: 49944.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella novicida (bacteria) / Gene: figC / Plasmid: pET28b / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / Variant (production host): Methionine auxotroph / References: UniProt: Q15EG8
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56 % / Description: cubic like crystal
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.7 M Ammonium sulfate, 0.085 M Hepes pH 7.5, 1.7% PEG400, 15% Glycerol, and 10 mM DTT

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: liquid nitrogen stream / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793217 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2015 / Details: Sagittal focusing 2nd crystal
Radiation	Monochromator: Si (111) Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793217 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 237296 / % possible obs: 99.9 % / Redundancy: 13.2 % / B_iso Wilson estimate: 21.98 Å² / R_pim(I) all: 0.021 / Net I/σ(I): 35.95
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 2.41 / Num. unique obs: 6761 / CC_1/2: 0.741 / R_pim(I) all: 0.322 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-2000		data reduction
HKL-2000		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.05→40.65 Å / SU ML: 0.1696 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1992	3639	1.53 %
R_work	0.1737	233644	-
obs	0.1741	237283	90.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→40.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13163	0	112	683	13958

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0046	13540
X-RAY DIFFRACTION	f_angle_d	0.661	18338
X-RAY DIFFRACTION	f_chiral_restr	0.0452	2121
X-RAY DIFFRACTION	f_plane_restr	0.0033	2308
X-RAY DIFFRACTION	f_dihedral_angle_d	11.0281	1800

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 (%)
2.05-2.08	0.2463	72	0.236	4752	X-RAY DIFFRACTION	47.79
2.08-2.11	0.2538	82	0.2242	5386	X-RAY DIFFRACTION	55
2.11-2.14	0.2536	95	0.2166	5976	X-RAY DIFFRACTION	59.95
2.14-2.17	0.2261	106	0.2006	6583	X-RAY DIFFRACTION	66.85
2.17-2.2	0.2106	106	0.1971	7214	X-RAY DIFFRACTION	72.9
2.2-2.24	0.2217	127	0.1933	7970	X-RAY DIFFRACTION	80.5
2.24-2.28	0.2231	138	0.1957	8757	X-RAY DIFFRACTION	88.74
2.28-2.32	0.2223	147	0.1953	9426	X-RAY DIFFRACTION	95.13
2.32-2.36	0.2585	151	0.1935	9752	X-RAY DIFFRACTION	98.35
2.36-2.41	0.2144	152	0.1858	9780	X-RAY DIFFRACTION	99.33
2.41-2.46	0.2253	151	0.1873	9797	X-RAY DIFFRACTION	99.68
2.46-2.52	0.1903	155	0.1851	9937	X-RAY DIFFRACTION	99.85
2.52-2.58	0.2134	149	0.1802	9825	X-RAY DIFFRACTION	99.89
2.58-2.65	0.1961	151	0.1849	9935	X-RAY DIFFRACTION	99.95
2.65-2.73	0.2234	155	0.1841	9850	X-RAY DIFFRACTION	99.95
2.73-2.82	0.2302	158	0.1824	9918	X-RAY DIFFRACTION	100
2.82-2.92	0.2013	148	0.1836	9826	X-RAY DIFFRACTION	100
2.92-3.04	0.1843	153	0.1835	9921	X-RAY DIFFRACTION	99.99
3.04-3.17	0.2311	161	0.19	9868	X-RAY DIFFRACTION	99.99
3.17-3.34	0.2089	149	0.1791	9891	X-RAY DIFFRACTION	100
3.34-3.55	0.2179	157	0.1677	9875	X-RAY DIFFRACTION	100
3.55-3.82	0.1811	151	0.1552	9877	X-RAY DIFFRACTION	100
3.83-4.21	0.1277	160	0.1445	9892	X-RAY DIFFRACTION	99.99
4.21-4.82	0.1661	152	0.1318	9898	X-RAY DIFFRACTION	100
4.82-6.07	0.1816	157	0.1572	9856	X-RAY DIFFRACTION	100
6.07-40.65	0.2047	156	0.1779	9882	X-RAY DIFFRACTION	99.78

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	0.550502277236	-0.563730645149	-0.328757169103	0.577995097141	0.293368329386	0.870335886418	0.0442669318629	0.0637352073229	-0.18108478363	-0.413422237386	0.0562623684688	-0.468337897466	0.212655103148	0.548157711787	-0.161917214829	0.327897855081	0.0967388974982	0.177230100898	0.557541812444	-0.295115880991	0.754211139562	65.2217656736	10.8699784144	37.7285918912
2	0.775052949624	-0.213404547174	0.223084933051	0.672429353698	0.202236666934	0.898847451329	-0.0502400088607	0.234727511136	-0.0369775250189	-0.737310335334	0.211097803392	-0.257359423796	-0.134540508812	0.335643814776	-0.129979755189	0.672135631187	-0.114735707569	0.160839004189	0.228951964469	-0.0740589294618	0.267861388473	42.6511720337	25.324246921	23.8802206571
3	1.15513553285	-0.731668297347	0.297702444162	5.7489219911	-1.81990303417	1.57169711556	-0.187815592993	-0.0956338919417	-0.143268042897	-0.243791835486	0.358913320888	0.385531710233	-0.0805435528941	-0.303842029109	-0.0860167537173	0.604381306835	-0.0695284641648	-0.0842269025733	0.270274319181	0.0402155332436	0.261097794261	22.6744967906	25.7835596626	26.8926487595
4	0.559915076342	-0.167445168911	0.145311863191	1.10476779984	0.343960620744	0.501718649219	0.0493762106619	0.0446223323417	-0.193007698701	-0.828744132116	0.158490169774	0.166160392369	0.163303701801	0.0475430471706	0.104792757911	0.841720972216	-0.12945730618	-0.116492682346	0.0762500634077	-0.0306408352438	0.321358849138	30.9625796293	13.7549456479	22.1111422423
5	1.22868995798	-0.141789588576	1.20740428143	0.508550764584	-0.796694475688	2.11288838189	0.106404396719	-0.251820599904	-0.409092641987	0.0182895449369	0.305090288993	-0.372356186062	0.592047103385	0.246415864603	-0.106428997847	0.396917456436	0.191669171986	-0.0509908666171	0.363891698583	-0.13393716697	0.677762996727	55.9615024789	6.81852497768	50.9319345158
6	1.60153795142	-0.576213547748	-0.36085706475	1.52233822898	0.487007545233	1.24668951124	-0.0135451832786	0.137845940648	-0.0281191461055	-0.420095733059	0.318607718247	-0.496053772109	-0.176856824506	0.701855260402	-0.221671977184	0.345857192526	-0.0399333408393	0.161041872731	0.396393902878	-0.166414996224	0.482632373957	56.7169527514	21.5141329187	39.5232383831
7	0.829003695796	-0.452522623786	0.307684216714	1.34448573918	-0.645939985841	1.38324866139	-0.0362581310944	0.264491147167	-0.112653507205	-0.262399951332	-0.0239317300311	0.0334525340426	0.181517956195	0.0923641823391	0.0295511737316	0.13999951054	-0.0648208698799	0.0229653724752	0.251726713275	-0.0635367455362	0.141504809791	47.5602935323	65.4576048042	1.10491154509
8	1.28312984824	0.351944463021	-0.072234836224	1.77683335172	0.330165000885	0.452115539733	-0.147410695173	0.209064835232	0.10377162939	-0.185285861374	0.0584468204845	-0.30079801945	-0.287497127125	0.381354730006	-0.136910209562	0.245385239809	-0.280479402814	-0.00378196769249	0.431562021252	0.0689451687602	0.139646143802	57.4150901595	86.5830065187	-0.558778336529
9	3.08362891963	0.755490963657	-0.979041778057	2.29134499623	-0.0472177413775	1.32695121807	-0.107213353821	0.279877329896	0.245725036816	-0.340245550904	-0.11423929425	0.142248068805	-0.459063979923	0.100600872169	-0.0221904872533	0.440735452219	-0.14343038532	-0.148086761451	0.273200410815	0.0969944798218	0.205710716998	46.6218975885	97.6761911734	0.768884997904
10	0.829609368372	-0.198817453677	0.557628346767	0.994994521695	-0.151211043755	1.46219621841	-0.130976251422	0.129778388173	0.0240042507073	-0.0180515873811	0.0157713583196	0.179026445835	-0.217332611772	-0.0701171171332	0.0331789263408	0.0960981513424	-0.0432439391505	-0.0105570688556	0.16318845622	-0.0277927291049	0.158402597489	39.1357989908	75.5067864441	7.8315464045
11	1.09579705065	-0.0689946606588	-0.144145100146	1.70002275229	1.22715719328	2.7570772203	-0.0133421459	0.194247354137	-0.194260393714	-0.120205519525	0.0977799861409	-0.0982104906829	-0.0440682347635	0.4369678862	-0.1085645431	0.115687816513	-0.017804049525	0.0530842097376	0.257807854175	-0.055882613243	0.168216337452	58.1004982294	64.4512384866	12.362672385
12	5.54235557211	-0.978040169632	-1.73079153042	2.24658254507	1.15000314201	5.3221043766	0.0420952156665	-0.0518784176603	0.130675375247	-0.290624162064	-0.0647829319816	0.158738285243	-0.344659839473	-0.395010179543	-0.0170215629239	0.250383341955	0.0552885640577	-0.0194836743475	0.145530046029	-0.0267287432572	0.143736178944	27.3345875412	42.4442493121	53.8818137148
13	0.918554751738	-0.364047112908	-0.133579160035	0.837286535844	0.42524554941	0.827418149598	-0.0996016810815	-0.269901322889	-0.116174201252	0.278355760054	0.57610146343	-0.63118609069	0.353823284511	0.733767733877	-0.0337177447538	0.200614876831	0.303790179812	-0.103583701113	0.516487301027	-0.197163897594	0.533317540014	55.8811638124	25.3699199547	67.7069965741
14	1.26672002758	-0.621126487644	0.154002442663	1.27667681321	-0.319034919256	1.54256101845	-0.126419214143	-0.361962431901	-0.265787085035	0.504117630912	0.321416591789	-0.199709534457	0.569358865872	0.382106757122	-0.262802006217	0.454250070712	0.254269252955	-0.0868488851484	0.331925838323	0.0320651295341	0.317961945621	45.3888636645	22.5933287875	76.7091476549
15	2.36551909002	0.155387276524	1.34425365866	1.47797834549	-0.025253939846	2.80054822201	0.0638945793089	-0.106403245937	-0.270635785531	-0.263706368774	0.0744642280845	0.0998583542921	0.30793420446	-0.464452224911	-0.106357990071	0.208059912002	-0.0422926465295	0.0037883780419	0.158047901204	0.0174360777266	0.184162294015	25.6435286459	28.7849248534	47.9910422044
16	0.740575196844	-0.157628386559	-0.429090145654	1.62955970236	1.26999325507	2.25966685363	-0.0376406578923	0.0413720635519	-0.0363376914111	-0.403610392575	0.311752093256	-0.132177608111	-0.351130769047	0.272666330683	-0.201941710944	0.307877450503	-0.0524986976444	0.107704327592	0.163267809142	-0.0270909274673	0.192634705584	41.7553036917	39.7914735928	48.1176058337
17	1.3655868219	-0.600859527988	-0.374729518077	4.14054000464	2.12312998147	4.36814858715	-0.197357826407	0.104163252861	0.302296475582	-0.132819556202	0.0514535920899	-0.0260378370298	-0.446131972714	0.187098438955	-0.0222690386393	0.157221322008	-0.0908384222796	-0.0805766021877	0.204613558407	0.064105714632	0.162353507049	63.6156265994	99.8603675512	27.4670930308
18	0.864780891874	0.322377708858	-0.0857501289568	1.36380860128	-0.0406555856199	0.841993853364	-0.0102365231009	0.0133619482742	-0.0807408867166	0.114851706416	0.00967081004329	-0.250463237468	0.0156426734696	0.222165899035	-0.00458954890996	0.0654251935472	-0.0228781262642	-0.0137396019442	0.148164154095	0.00996600421906	0.121115068895	65.7225608169	74.5259777317	38.2859891081
19	4.07739262177	-0.702178725197	-0.510749949434	3.80044938897	0.217099179877	2.92357971994	0.00586759405629	0.0671982037616	-0.447801098802	0.115246266042	0.0219395530824	-0.230860688968	0.47736684206	0.179356254207	-0.0378754279011	0.244923775669	0.0326775785905	0.0155442135082	0.130487543354	0.0188952172789	0.228235269555	59.8487859733	53.8984841351	37.0747561371
20	5.8431450143	-3.96856966993	-0.944579098145	5.44746154938	1.04762899853	2.13298845398	0.0362887780368	-0.182225450612	-0.06109463537	0.127831436682	-0.0183791903376	0.233175561979	0.13337474471	-0.117969507868	-0.00309521724577	0.160129337514	-0.0736067771906	0.0493758031117	0.177888330268	0.0402160740472	0.192875620334	48.9766400617	62.1902776944	43.699173438
21	0.894435846285	0.386117603813	0.020041136283	2.02165634609	-0.195885493296	1.09846707839	0.0665182255186	-0.21303943153	-0.122458169339	0.373191457674	-0.0595839354932	0.155026461573	0.126029559237	-0.0863012125255	-0.0144060178184	0.144913257075	-0.0404785085979	0.0412937629167	0.205112912638	0.0150233546671	0.138058037623	51.9123685462	70.6971651444	49.094652729
22	1.34113695818	-0.436107950176	0.289242877569	1.96624569602	-0.787412041101	2.18857824216	-0.10717924228	0.0547907096954	0.129295444484	-0.141269564644	0.0558033697148	0.335430023595	-0.362724366514	-0.236810091686	0.0894214322953	0.17238978413	-0.0288135537977	-0.07675503792	0.179696313084	0.016957285133	0.198169767835	50.0246066734	96.4688110617	22.2285910848
23	3.19443967724	1.53219771056	2.87180679842	1.48494173405	1.25558245206	2.89471945033	-0.00197520385794	0.353761388855	-0.0555842441348	-0.107611610987	0.161691338536	-0.137347934347	-0.0356082445808	0.461918889722	-0.158868181678	0.109081575956	-0.0764543797212	0.0244597108151	0.275923289715	-0.0223272892221	0.140508085537	66.2335607417	85.4075612014	20.5693906257

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 128 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 129 through 176 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 177 through 296 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 297 through 373 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 374 through 416 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 77 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 78 through 119 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 120 through 177 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 178 through 387 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 388 through 417 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 0 through 29 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 30 through 206 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 207 through 296 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 297 through 387 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 388 through 416 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 0 through 29 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 30 through 110 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 111 through 141 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 142 through 165 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 166 through 296 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 297 through 387 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 388 through 417 )

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