PDB-5hjx: Structure function studies of R. palustris RubisCO (A47V mutant; ...

ID or keywords:

Entry

Database: PDB / ID: 5hjx

Title

Structure function studies of R. palustris RubisCO (A47V mutant; CABP-bound)

Components

Ribulose bisphosphate carboxylase

Keywords

LYASE / RubisCO / hexamer

Function / homology

Function and homology information

ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function

Biological species

Rhodopseudomonas palustris (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.799 Å

Authors

Arbing, M.A. / Shin, A. / Satagopan, S. / North, J.A. / Tabita, F.R.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM095742	United States
Department of Energy (DOE, United States)	DE-FC02-02ER63421	United States

Citation

Journal: To Be Published
Title: Structure function studies of R. palustris RubisCO.
Authors: Arbing, M.A. / Satagopan, S. / Varaljay, V.A. / Shin, A. / Tabita, F.R.

History

Deposition	Jan 13, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5hjx.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb5hjx.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	5hjx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5hjx_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5hjx_full_validation.pdf.gz	2.2 MB	Display
Data in XML	5hjx_validation.xml.gz	128 KB	Display
Data in CIF	5hjx_validation.cif.gz	166.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hj/5hjx ftp://data.pdbj.org/pub/pdb/validation_reports/hj/5hjx	HTTPS FTP

-
Related structure data

Related structure data	5haoC 5hatC 5hjyC 5hk4C 5hqmC 5kozC 4lf1S 5han 5hql C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hqm-1 5hql-d 4lf1-d 5han-1 5c2g-d 5hao-d 4lf2-d 5han-2 5hjy-d 5hat-2 5hat-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#11 - Nov 2000 Rubisco similarity (13)

Deposited unit

A: Ribulose bisphosphate carboxylase

B: Ribulose bisphosphate carboxylase

C: Ribulose bisphosphate carboxylase

D: Ribulose bisphosphate carboxylase

E: Ribulose bisphosphate carboxylase

F: Ribulose bisphosphate carboxylase

hetero molecules

319 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	75.960, 100.250, 100.380
Angle α, β, γ (deg.)	113.06, 108.07, 88.89
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ribulose bisphosphate carboxylase / RuBisCO Mass: 52785.395 Da / Num. of mol.: 6 / Mutation: A47V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6N0W9, ribulose-bisphosphate carboxylase
#2: Sugar	ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Type: saccharide / Mass: 356.115 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₃P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1637 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.3 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM NaHCO3. Reservoir solution: 20-24% PEG 3350, 200 mM sodium sulfate, 100 mM Bis-tris propane pH 7.0-8.0 PH range: 7-8

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9797 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9797 Å / Relative weight: 1

Reflection

Resolution: 1.799→87.22 Å / Num. obs: 208202 / % possible obs: 87 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / B_iso Wilson estimate: 25.69 Å² / R_merge F obs: 0.994 / R_merge(I) obs: 0.055 / R_rim(I) all: 0.078 / Χ²: 1.03 / Net I/σ(I): 7.98 / Num. measured all: 388868

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.799-1.85	1.8	0.727	0.385	1.9	27621	17732	15537	0.544	87.6
1.85-1.9		0.768	0.346	2.35	29770	17306	15624	0.489	90.3
1.9-1.95		0.82	0.323	2.75	26132	16769	13896	0.456	82.9
1.95-2.01		0.893	0.207	3.7	28016	16256	14894	0.293	91.6
2.01-2.08		0.927	0.179	4.37	24797	15774	13319	0.253	84.4
2.08-2.15		0.943	0.144	5.02	24929	15312	13675	0.204	89.3
2.15-2.23		0.963	0.118	5.73	23532	14795	13114	0.167	88.6
2.23-2.32		0.967	0.108	7.12	22231	14100	11629	0.152	82.5
2.32-2.43		0.977	0.084	8.32	23677	13614	12401	0.119	91.1
2.43-2.54		0.982	0.073	9.22	21813	13008	11521	0.103	88.6
2.54-2.68		0.985	0.065	10.14	19773	12313	10546	0.092	85.6
2.68-2.84		0.987	0.057	11.04	17694	11748	9854	0.081	83.9
2.84-3.04		0.989	0.05	12.74	18913	11055	9894	0.071	89.5
3.04-3.28		0.99	0.045	14.1	17096	10181	8904	0.063	87.5
3.28-3.6		0.991	0.042	15.16	15150	9397	7962	0.06	84.7
3.6-4.02		0.991	0.041	15.77	12775	8539	6960	0.058	81.5
4.02-4.65		0.992	0.037	16.56	12054	7497	6458	0.052	86.1
4.65-5.69		0.991	0.038	16.87	10730	6330	5598	0.054	88.4
5.69-8.05		0.991	0.04	16.66	7726	4916	4135	0.056	84.1
8.05-87.22		0.989	0.042	17.74	4439	2703	2281	0.059	84.4

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LF1

4lf1

Resolution: 1.799→87.22 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2093	20803	10 %	Random selection
R_work	0.1828	-	-	-
obs	0.1855	208046	87.1 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.799→87.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21142	0	132	1637	22911

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	21832
X-RAY DIFFRACTION	f_angle_d	0.827	29518
X-RAY DIFFRACTION	f_dihedral_angle_d	11.38	7836
X-RAY DIFFRACTION	f_chiral_restr	0.033	3070
X-RAY DIFFRACTION	f_plane_restr	0.004	3908

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 (%)
1.7991-1.8196	0.3062	654	0.2866	5878	X-RAY DIFFRACTION	81
1.8196-1.841	0.3067	737	0.2741	6634	X-RAY DIFFRACTION	93
1.841-1.8634	0.2814	739	0.2502	6650	X-RAY DIFFRACTION	93
1.8634-1.887	0.2796	695	0.2705	6266	X-RAY DIFFRACTION	87
1.887-1.9119	0.2944	712	0.275	6403	X-RAY DIFFRACTION	89
1.9119-1.938	0.3465	630	0.2961	5671	X-RAY DIFFRACTION	79
1.938-1.9657	0.28	702	0.2467	6322	X-RAY DIFFRACTION	88
1.9657-1.9951	0.249	725	0.2209	6516	X-RAY DIFFRACTION	91
1.9951-2.0263	0.2593	736	0.2217	6627	X-RAY DIFFRACTION	92
2.0263-2.0595	0.2623	718	0.2254	6457	X-RAY DIFFRACTION	90
2.0595-2.095	0.279	617	0.2404	5553	X-RAY DIFFRACTION	77
2.095-2.1331	0.2387	711	0.2085	6395	X-RAY DIFFRACTION	89
2.1331-2.1741	0.2508	708	0.2106	6372	X-RAY DIFFRACTION	88
2.1741-2.2185	0.2295	703	0.2054	6326	X-RAY DIFFRACTION	89
2.2185-2.2667	0.254	628	0.2185	5653	X-RAY DIFFRACTION	79
2.2667-2.3195	0.2204	700	0.1887	6301	X-RAY DIFFRACTION	88
2.3195-2.3775	0.2106	734	0.1854	6613	X-RAY DIFFRACTION	92
2.3775-2.4418	0.2081	719	0.1768	6488	X-RAY DIFFRACTION	91
2.4418-2.5136	0.212	703	0.181	6320	X-RAY DIFFRACTION	88
2.5136-2.5948	0.2115	706	0.1745	6353	X-RAY DIFFRACTION	89
2.5948-2.6875	0.2229	665	0.1843	5984	X-RAY DIFFRACTION	84
2.6875-2.7951	0.2108	683	0.183	6141	X-RAY DIFFRACTION	86
2.7951-2.9223	0.2285	688	0.1887	6196	X-RAY DIFFRACTION	86
2.9223-3.0764	0.2261	706	0.1848	6348	X-RAY DIFFRACTION	89
3.0764-3.2692	0.2048	698	0.1784	6281	X-RAY DIFFRACTION	88
3.2692-3.5216	0.1924	674	0.1722	6077	X-RAY DIFFRACTION	85
3.5216-3.876	0.1655	668	0.1538	6012	X-RAY DIFFRACTION	84
3.876-4.4368	0.1577	661	0.1398	5959	X-RAY DIFFRACTION	83
4.4368-5.5898	0.1635	707	0.1417	6373	X-RAY DIFFRACTION	89
5.5898-87.3226	0.1848	676	0.1688	6074	X-RAY DIFFRACTION	85

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	2.063	0.0504	-0.1849	0.3533	0.1722	0.3443	-0.0021	-0.4604	-0.6922	0.0948	-0.0191	-0.0004	0.1289	0.0472	0.0269	0.2994	0.0078	0.0024	0.2187	0.1821	0.3891	-27.7646	-117.4985	-2.086
2	2.0558	0.0794	0.0332	0.5217	-0.0096	0.2642	0.0403	0.2784	-0.6926	-0.044	0.0078	-0.0038	0.0982	0.0929	-0.0291	0.2666	0.0287	-0.0212	0.1524	-0.0942	0.3768	-14.0487	-117.0751	-26.3831
3	2.2435	0.1542	-0.1517	0.6889	-0.2325	0.4966	0.0992	0.967	-0.1219	-0.1808	-0.0546	0.0487	0.0204	0.0046	-0.011	0.3008	0.0499	-0.0151	0.5896	-0.0316	0.0887	-29.6265	-90.9161	-50.1684
4	2.047	0.1919	0.167	0.3807	0.0523	0.7362	0.0055	0.555	0.6741	-0.0783	-0.0001	0.0744	-0.1899	0.0413	-0.0148	0.3251	0.0132	0.0376	0.2771	0.2106	0.3668	-27.8388	-65.4066	-39.0781
5	2.0669	0.0315	0.087	0.4352	0.0755	0.5139	0.023	-0.3685	0.7199	0.056	-0.0033	0.0583	-0.1211	-0.0515	0.0187	0.2869	-0.0025	0.0494	0.1906	-0.1375	0.4016	-43.3003	-64.8274	-3.7993
6	2.0507	-0.044	-0.1381	0.5849	0.0206	0.3451	0.0507	-0.8612	0.2413	0.1759	-0.0037	0.0071	-0.0487	0.0536	-0.0184	0.3225	-0.0345	0.028	0.5356	-0.1058	0.1406	-29.4073	-82.156	13.1337

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi