PDB-27jx: Crystal structure of the HVM1 in complex with oxovanadium, succin...

ID or keywords:

Entry

Database: PDB / ID: 27jx

Title

Crystal structure of the HVM1 in complex with oxovanadium, succinic acid and helvamide.

Components

oxidoreductase

Keywords

OXIDOREDUCTASE / AKG / SIN / VVO

Function / homology

: / SUCCINIC ACID / oxovanadium(2+)

Function and homology information

Biological species

Aspergillus rugulosus (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96001018958 Å

Authors

Zuo, J.Y. / Zhang, Z.M.

Funding support

1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2026
Title: Radical Mechanism and Stereochemical Control in Consecutive C-C Bond Formation by the Nonheme Iron Enzyme Hvm1.
Authors: Zhou, S. / Zhang, J. / Zuo, J.Y. / Yu, J. / Du, Y.F. / Wang, R. / Wu, C. / Zhang, G. / Shang, A. / Zhou, P. / Wang, Y. / Zhang, Z.M. / Li, H. / Liu, H.

History

Deposition	Jun 3, 2026	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Sep 30, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	27jx.cif.gz	294.4 KB	Display	PDBx/mmCIF format
PDB format	pdb27jx.ent.gz		Display	PDB format
PDBx/mmJSON format	27jx.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/7j/27jx ftp://data.pdbj.org/pub/pdb/validation_reports/7j/27jx	HTTPS FTP

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Related structure data

Related structure data	9xpoC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: oxidoreductase

B: oxidoreductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	72.688, 93.898, 113.048
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
Int Tables number	18
Space group name H-M	P2₁22₁
Space group name Hall	P22ab(y,z,x)
Symmetry operation	#1: x,y,z #2: x+1/2,-y,-z+1/2 #3: -x,y,-z #4: -x+1/2,-y,z+1/2

#1: Protein	oxidoreductase Mass: 32103.834 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus rugulosus (mold) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₄
#3: Chemical	ChemComp-VVO / oxovanadium(2+) Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV
#4: Chemical	ChemComp-A1E05 / 1-[(2~{S},5~{Z})-5-[(7-methoxy-1,3-benzodioxol-5-yl)methylidene]-4-(phenylcarbonyl)-2-(phenylmethyl)piperazin-1-yl]ethanone / Helvamide Mass: 484.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₂₈N₂O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.99 Å³/Da / Density % sol: 58.93 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion Details: 0.1M sodium chloride, 0.1M HEPES pH 7.5, 1.2M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.9786 Å
Detector	Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 29, 2026
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.88→72.23 Å / Num. obs: 55791 / % possible obs: 99.2 % / Redundancy: 8.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.131 / Net I/σ(I): 10.5
Reflection shell	Resolution: 1.88→1.99 Å / Num. unique obs: 55791 / CC_1/2: 0.926

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692+SVN	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96001018958→48.426740445 Å / SU ML: 0.188348930407 / Cross valid method: NONE / σ(F): 1.33790291863 / Phase error: 26.5956708051

	R_factor	Num. reflection	% reflection
R_free	0.207883312768	1778	3.18689394347 %
R_work	0.169358549138	54013	-
obs	0.170580450222	55791	99.1857633025 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.3548712098 Å²

Refinement step

Cycle: LAST / Resolution: 1.96001018958→48.426740445 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4408	0	40	613	5061

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0183184668851	4562
X-RAY DIFFRACTION	f_angle_d	1.22118569045	6190
X-RAY DIFFRACTION	f_chiral_restr	0.0537665557762	687
X-RAY DIFFRACTION	f_plane_restr	0.00652578368081	803
X-RAY DIFFRACTION	f_dihedral_angle_d	13.972459784	1712

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 (%)
1.97-2.013	0.302429534983	135	0.233201989638	4126	X-RAY DIFFRACTION	99.6725146199
2.013-2.0722	0.249871504413	134	0.217638537594	4075	X-RAY DIFFRACTION	99.4095418044
2.0722-2.1391	0.269675119101	137	0.208839643908	4141	X-RAY DIFFRACTION	99.3959107807
2.1391-2.2156	0.274157914875	136	0.189432837852	4099	X-RAY DIFFRACTION	99.6001881468
2.2156-2.3043	0.200789762579	134	0.177246113258	4138	X-RAY DIFFRACTION	99.6501049685
2.3043-2.4092	0.205207053825	137	0.172143706866	4167	X-RAY DIFFRACTION	99.7913285416
2.4092-2.5362	0.198852845915	136	0.163760980219	4120	X-RAY DIFFRACTION	99.74220764
2.5362-2.6951	0.252523236443	137	0.172739309762	4171	X-RAY DIFFRACTION	99.8609179416
2.6951-2.9031	0.224019009215	138	0.178038293716	4168	X-RAY DIFFRACTION	99.6759259259
2.9031-3.1952	0.210117518556	138	0.170856509507	4184	X-RAY DIFFRACTION	99.9306358382
3.1952-3.6574	0.18142614378	136	0.154903474395	4126	X-RAY DIFFRACTION	99.765917603
3.6574-4.6074	0.16220109251	135	0.131459562528	4084	X-RAY DIFFRACTION	99.0608123973
4.6074-48.426	0.187644108749	145	0.167259596921	4414	X-RAY DIFFRACTION	99.2165397171

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	1.69973620964	-0.170235250838	0.179650528363	1.67273576719	-0.404839450589	1.42962421856	-0.0271113818847	0.238459586809	-0.0773949987892	-0.12528889161	0.0592845541462	-0.137118036695	-0.0194185233528	0.0543215261124	-0.0174396700784	0.183051507892	-0.00657036835592	-0.00758376434548	0.198839178222	-0.0677991618173	0.164646191494	7.31570154096	91.0752835688	13.3045836549
2	1.76103245793	0.873847828638	-0.0626358923682	1.09779436436	0.585613287017	0.62731463653	-0.0128264157164	-0.0528406308754	0.0759674425168	0.0718970941173	-0.0107382785211	0.103738173499	0.0895719526048	0.020040909605	0.0125069494462	0.154078518914	-0.0144198701107	0.00723799411343	0.157400997271	0.025028316093	0.0899518570339	-6.54893425505	99.5774957931	32.5865346432
3	0.304291963901	0.100139544402	-0.00611496726375	0.831877119781	0.470707047559	0.290617743666	-0.0539368044893	0.0588498487506	0.00483042000792	-0.10812244447	0.0562919797527	0.0148696626414	-0.00261254924315	-0.00577297517575	0.00566542766017	0.182542925576	-0.00969745077095	-0.00543188022034	0.184244327922	0.0154154390988	0.115770756235	0.804601208967	104.408531298	18.1068394695
4	1.35619901172	0.589748869255	-0.284755808445	1.11286469213	-0.105937404742	0.684428983377	-0.114695822494	0.404852879919	-0.083147665237	0.00384654190633	0.187221744816	0.168929267727	0.0113400737014	-0.110097811459	-0.04237599769	0.180041908569	-0.0386094883461	-0.0225119103403	0.258594811481	0.00961074328837	0.100006768984	-6.84688565247	94.0799157151	13.0519152552
5	0.767342540473	0.312268496211	0.119891824877	1.41274451707	-0.0132930876074	0.284203217122	0.0163527809379	-0.102536473969	0.0646064800333	0.105088842214	-0.00971911128896	-0.0600707326837	0.012699073277	0.00663715282018	-0.0123909775566	0.151578464056	-0.0021046702269	-0.00548316521685	0.150521870804	-0.013122145281	0.112346995248	9.41353628088	110.991459468	31.3603807984
6	2.13700688593	-0.115618582417	-0.649295449928	1.67402239688	0.175216638175	1.58189483069	0.036227335251	0.227288578354	0.383588655624	-0.248990599182	-0.0165446157462	0.0908545608052	0.0365978291283	-0.0859377566344	-0.0294978679036	0.236196829829	0.00201515056042	0.00892991689221	0.21156359207	0.0716934590104	0.389750062351	1.08801978019	143.551058462	13.0676480478
7	1.31958964292	0.508640674002	0.0936834024965	1.05758906444	-0.467535816488	0.472761056724	-0.000635926810953	-0.0715927155003	0.166944563316	0.105377856016	-0.0263010118239	-0.0490103543732	-0.0920818485481	0.0268454147818	0.0409197368667	0.192855315372	-0.0128431398067	0.000434695834614	0.18146081055	-0.0462065770384	0.266506881974	14.9679662398	135.211496637	32.4103753461
8	0.752353455555	0.0997187126676	0.190472788154	1.49876994024	-0.149176346019	0.742293194556	-0.0343471031269	0.0419713654457	0.130202028973	-0.165779117785	0.0991275305542	0.0668680521996	-0.0758228606532	-0.0764400792812	-0.0520685200341	0.185721266885	0.0107858872686	-0.0116496958371	0.183192657734	0.0246259955408	0.305695059522	1.59774676158	131.943884904	22.4412592007
9	0.230007491494	-0.0704014000673	-0.190884450681	1.34067312759	-0.340079737728	0.297063450857	-0.0451743784856	0.0543927661934	0.0977107367882	-0.308551938585	0.0817832305803	-0.242447164001	-0.0489103257308	0.0117781840513	-0.0247377793249	0.224280507204	-0.0092541829202	0.0134435640996	0.190992841672	0.00293081436617	0.265396424187	11.9089766277	128.970830037	14.7817440511
10	1.68893844246	0.723957650665	0.177067957445	1.08388952105	-0.239167933174	0.846975810611	-0.108043177886	0.284367238897	0.0695761333354	-0.165692521594	0.142927898524	-0.227261153699	0.00920245144031	0.104582397384	-0.0426105272221	0.221195591125	-0.0191609056136	0.0516974635842	0.224421415239	0.0153801830425	0.353910173541	15.24582518	140.447886047	12.9103208609
11	1.04298935415	0.203716576489	-0.230906797314	1.79052411464	-0.124312257258	0.578361040526	0.0453991876225	-0.0696249983852	0.138022146779	0.0846217485583	0.0156225881996	0.23674905489	-0.0147473371653	-0.0362837066562	-0.0504045410546	0.158666502206	0.000643121699518	-0.000196221897954	0.16792918733	-0.0148975803131	0.233279637573	-1.01443705816	123.782711435	31.4031433008

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 158 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 159 through 218 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 219 through 288 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 8 through 40 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 41 through 95 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 96 through 122 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 123 through 158 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 159 through 218 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 219 through 288 )

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