PDB-7z1u: Biochemical implications of the substitution of a unique cysteine...

ID or keywords:

Entry

Database: PDB / ID: 7z1u

Title

Biochemical implications of the substitution of a unique cysteine residue in sugar beet phytoglobin BvPgb 1.2

Components

Non-symbiotic hemoglobin class 1

Keywords

OXYGEN BINDING / Phytoglobin / globin fold / redox balance / cysteine substitution

Function / homology

Function and homology information

oxygen binding / heme binding / metal ion binding
Similarity search - Function

Biological species

Beta vulgaris (beet)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.24 Å

Authors

Nyblom, M. / Christensen, S. / Leiva Eriksson, N. / Bulow, L.

Funding support

Sweden, 2items

Citation

Journal: Antioxidants / Year: 2022
Title: Oxidative Implications of Substituting a Conserved Cysteine Residue in Sugar Beet Phytoglobin BvPgb 1.2.
Authors: Christensen, S. / Groth, L. / Leiva-Eriksson, N. / Nyblom, M. / Bulow, L.

History

Deposition	Feb 25, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 7, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7z1u.cif.gz	162.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7z1u.ent.gz	108.2 KB	Display	PDB format
PDBx/mmJSON format	7z1u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7z1u_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7z1u_full_validation.pdf.gz	1.3 MB	Display
Data in XML	7z1u_validation.xml.gz	13.6 KB	Display
Data in CIF	7z1u_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/7z1u ftp://data.pdbj.org/pub/pdb/validation_reports/z1/7z1u	HTTPS FTP

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Related structure data

Related structure data	7zosC 3zhwS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#206 - Feb 2017 Globin Evolution similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#206 - Feb 2017
Globin Evolution
similarity (1)
#41 - May 2003
Hemoglobin
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)

Deposited unit

A: Non-symbiotic hemoglobin class 1

B: Non-symbiotic hemoglobin class 1

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, Gel filtration (Size Exclusion Chromatography) was conducted on both wild-type and C86A mutant to investigate any structural differences. Also, NMR relaxation studies was ...Evidence: gel filtration, Gel filtration (Size Exclusion Chromatography) was conducted on both wild-type and C86A mutant to investigate any structural differences. Also, NMR relaxation studies was conducted for the wild-type as a complement to the crystallization data.

Unit cell

Length a, b, c (Å)	36.850, 73.920, 62.830
Angle α, β, γ (deg.)	90.000, 105.050, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain 'A' and (resid 8 through 51 or resid 60 through 91 or resid 96 through 160 or resid 1163))	A	8 - 51
1	2	1	(chain 'A' and (resid 8 through 51 or resid 60 through 91 or resid 96 through 160 or resid 1163))	A	60 - 91
1	3	1	(chain 'A' and (resid 8 through 51 or resid 60 through 91 or resid 96 through 160 or resid 1163))	A	96 - 160
1	4	1	(chain 'A' and (resid 8 through 51 or resid 60 through 91 or resid 96 through 160 or resid 1163))	A	1163
2	5	1	(chain 'B' and (resid 8 through 160 or resid 1163))	B	8 - 51
2	6	1	(chain 'B' and (resid 8 through 160 or resid 1163))	B	60 - 91
2	7	1	(chain 'B' and (resid 8 through 160 or resid 1163))	B	96 - 160
2	8	1	(chain 'B' and (resid 8 through 160 or resid 1163))	B	1163

#1: Protein	Non-symbiotic hemoglobin class 1 Mass: 19221.236 Da / Num. of mol.: 2 / Mutation: C86A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Beta vulgaris (beet) / Gene: Bv9_224250_aayd.t2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5QR23
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.15 Å³/Da / Density % sol: 42.8 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid) pH 8.0, 25 % (w/v) PEG 1500.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97996 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97996 Å / Relative weight: 1
Reflection	Resolution: 2.242→60.675 Å / Num. obs: 15684 / % possible obs: 99.9 % / Redundancy: 7 % / B_iso Wilson estimate: 54.7 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / Net I/σ(I): 12.7
Reflection shell	Resolution: 2.242→2.281 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.874 / Num. unique obs: 779 / CC_1/2: 0.953 / % possible all: 100

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
autoPROC		data processing
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	1.14_3260	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3zhw.pdb

3zhw

Resolution: 2.24→35.59 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 44.8238 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2881	797	5.12 %
R_work	0.2625	14761	-
obs	0.264	15558	99.08 %

Solvent computation

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

Displacement parameters

B_iso mean: 105.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.24→35.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2293	0	86	10	2389

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	2436
X-RAY DIFFRACTION	f_angle_d	0.5344	3296
X-RAY DIFFRACTION	f_chiral_restr	0.0358	354
X-RAY DIFFRACTION	f_plane_restr	0.0032	397
X-RAY DIFFRACTION	f_dihedral_angle_d	13.7165	1434

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 (%)
2.24-2.38	0.4667	116	0.3919	2449	X-RAY DIFFRACTION	98.28
2.38-2.57	0.3526	99	0.3529	2442	X-RAY DIFFRACTION	98.6
2.57-2.82	0.3278	132	0.326	2446	X-RAY DIFFRACTION	98.47
2.82-3.23	0.3221	161	0.3104	2441	X-RAY DIFFRACTION	99.58
3.23-4.07	0.3159	131	0.2832	2485	X-RAY DIFFRACTION	99.77
4.07-35.59	0.2483	158	0.2109	2498	X-RAY DIFFRACTION	99.77

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	4.03098763641	-1.81989651887	0.280414958623	4.81977653416	-4.40343729979	6.41674978382	0.335299060556	-0.155673746604	0.616573248586	1.14721315288	0.00272270986799	0.694580929936	-1.08133357569	0.0245698335522	-0.0886943876627	1.03457121758	0.0550341102262	0.142442580029	0.31213752477	0.0229291869925	1.02391193586	7.53945589334	-0.274359385081	-23.9339402566
2	1.77507314324	0.775211914978	-2.30782112185	1.62979750318	-3.61110668726	8.04305500823	-1.6815181649	0.416924374851	1.14953205238	1.11247906007	-1.56570314962	-0.281806034094	-2.27134731511	1.54667547232	2.47650672002	1.02957205829	-0.0277381532669	-0.375627305545	0.754640907586	0.176559951462	1.4570835913	22.907814786	-9.92757899152	-24.0268060466
3	6.88128471541	-1.64338543426	3.24555607078	5.28139960097	-4.06834700101	9.54890439413	-0.117468810803	0.358906918037	0.333322347369	-0.482244407055	0.321685351049	0.546360607316	0.302566620434	-0.177718120977	-0.0633225381603	0.949156491034	-0.0542532503579	0.0068480597174	0.319662576409	0.13939710265	0.799447123194	5.83778280336	-2.43319061536	-34.6711279002
4	8.24458588403	0.885986273791	2.16681151931	3.5805704466	-3.87505162299	5.32109938096	0.0779574972204	1.36163823644	-1.6348903752	-1.84646272489	0.636749861202	0.763695939756	1.27473894547	1.46456383528	0.198924561855	1.27957059059	0.0390407667815	0.168477854713	0.293551061576	0.102170254451	0.791322231231	8.76651593101	-16.4731914873	-34.8532643089
5	5.66297518203	-0.103249252445	-0.440034954723	7.94268630137	-6.43152476416	5.42750083384	0.325518859379	-0.359132818656	-0.192980469575	1.86294686815	0.03407868313	0.530945996551	-1.1152797306	-0.48591056084	-0.34489917336	0.740221428114	0.122654252577	0.143209824067	0.40847237086	0.131481650574	0.709599786397	4.17496022972	-7.39743561325	-20.1177158669
6	9.7680238252	-4.29961586238	2.81109231117	6.29869022382	-3.7604251272	2.29855372867	0.101485421033	-1.49873507041	2.20638668981	2.45166394848	0.176033635062	-0.267077174739	-1.69323607983	-0.122838887253	-0.751205055021	2.29805931435	0.457415049354	0.788237954462	0.287665518072	-0.29013970147	0.863925803392	3.56099888369	8.18223455108	-16.1209247912
7	3.18770248089	-1.87771397847	0.3581441354	9.85223847757	3.01464158545	7.07383740369	0.596446821034	0.161366818509	-0.403601991309	-1.76003220416	0.470496018794	2.75509347164	-0.542880635137	-1.1960302052	-0.364120694986	0.873647300582	-0.00130722198721	-0.186082705044	0.541844239137	0.286778890833	1.14278556018	-1.49001292495	-7.56718437784	-29.8399117602
8	5.04357300553	0.7695034972	-1.71167627982	3.77726258543	-2.84928038024	5.18501176938	0.958037411115	-1.07899351306	0.676985058051	3.30769105223	0.265027157153	0.665057333333	-1.12602989009	-0.51850056642	-0.870203318297	2.27861597365	0.122365877994	0.37953206926	0.752797281537	0.060303750223	1.13389399846	3.96705271376	-15.3752542113	-0.105046497926
9	2.60849516264	-2.77563063014	4.6761972294	3.05297429326	-5.10543167685	8.50155533622	0.151586409465	-0.5693956924	2.99843400066	1.7693207822	0.845649453631	-0.0623775677882	-1.76428641855	-1.31072912348	-1.93432419431	0.716644752599	-0.201479823753	0.333427325998	1.06955067284	0.284814056409	2.45557883131	-12.0957471405	-18.0444971265	-8.02352466178
10	2.91569556247	1.01212533349	2.83450796467	8.49558220512	-2.97756522102	6.40104908175	1.62422430753	-2.23268838707	0.83375431755	2.21829205404	0.885945181247	1.93693013339	-2.93426779234	-2.32021848385	-1.51075331666	2.1494884808	0.0438112525162	0.344389755527	0.866777952225	0.191778465431	0.901953202047	4.32203004407	-23.0213705744	2.8315066201
11	5.66004137789	-1.69376570447	-1.0004662955	2.72330290553	-0.579666857063	2.91167257456	-0.034319038165	-1.97191437411	-1.37712562765	1.49880044396	1.45578204744	0.846214746252	1.84083720109	-0.528980735448	-1.28573375305	0.859775729251	-0.185811016302	-0.218780272285	0.6404157469	0.272890384637	1.04793683597	4.66837032928	-31.9721196006	-6.52940308136
12	3.23827481916	1.61306948922	-0.857651066981	3.55123636294	-2.99226249492	2.85471308214	0.685931194682	-1.16425160787	0.254714189702	2.07375764049	-0.0542111441736	0.586333228239	-1.15918125202	-0.904346718413	-0.80909756635	0.98736362418	0.10361854497	0.0653925292313	0.413795216317	0.0970525750334	0.724017905519	7.20120479188	-15.1363627168	-8.21616217899
13	4.68307594671	1.48085518945	0.0172425071717	3.38270788237	2.92220852407	4.61230643243	-0.345972149587	-0.125774451777	-0.0648082669259	0.884782667093	0.118248875274	1.48187875333	0.898735776553	-0.136180170115	0.259131529089	3.52133710782	-0.329839212226	0.358072682362	0.785820875122	-0.330189769741	1.75501666563	8.04677728389	-4.87179129473	2.88278898376
14	7.58819968407	1.41055877815	0.2645161465	2.2188098909	2.44654383903	5.76342895648	0.145012833184	-0.834816455279	0.335928746025	2.10922726771	-0.0401551738239	-0.89152844258	-0.427766366921	0.91174587486	-0.0546481821019	1.40195707502	-0.176876923354	-0.297546720501	0.629823289573	0.118649367762	0.747228158371	12.8584395385	-21.3304407786	-2.86746285733
15	3.02610032888	2.74891015824	0.388056360419	3.83095596878	2.05284713543	2.8234510828	-1.13399391379	0.241079792008	0.43068225445	1.36292774218	-0.191755524768	-1.18712810136	0.46242815726	0.476760596848	0.164781026295	0.877714276252	0.307204066235	0.173191712153	0.861995147538	-0.105825987932	1.18909553597	9.44055313963	-37.9629990967	-15.5282086702

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 96 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 97 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 126 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 127 through 134 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 135 through 160 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 8 through 49 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 50 through 64 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 65 through 86 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 87 through 110 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 111 through 126 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 127 through 134 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 135 through 156 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 157 through 161 )

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