PDB-2pen: Crystal structure of RbcX, crystal form I

ID or keywords:

Entry

Database: PDB / ID: 2pen

Title

Crystal structure of RbcX, crystal form I

Components

ORF134

Keywords

CHAPERONE / helix bundle / protein complex assembly

Function / homology

Function and homology information

ribulose bisphosphate carboxylase complex assembly / carboxysome / carbon fixation / photosynthesis / protein folding chaperone / protein homodimerization activity / cytoplasm
Similarity search - Function

Biological species

Synechococcus sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.8 Å

Authors

Saschenbrecker, S. / Bracher, A. / Vasudeva Rao, K. / Vasudeva Rao, B. / Hartl, F.U. / Hayer-Hartl, M.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structure and Function of RbcX, an Assembly Chaperone for Hexadecameric Rubisco.
Authors: Saschenbrecker, S. / Bracher, A. / Rao, K.V. / Rao, B.V. / Hartl, F.U. / Hayer-Hartl, M.

History

Deposition	Apr 3, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 10, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2pen.cif.gz	136.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2pen.ent.gz	106.6 KB	Display	PDB format
PDBx/mmJSON format	2pen.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2pen_validation.pdf.gz	466.2 KB	Display	wwPDB validaton report
Full document	2pen_full_validation.pdf.gz	477 KB	Display
Data in XML	2pen_validation.xml.gz	23.2 KB	Display
Data in CIF	2pen_validation.cif.gz	32.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/2pen ftp://data.pdbj.org/pub/pdb/validation_reports/pe/2pen	HTTPS FTP

-
Related structure data

Related structure data	2peiC 2pejC 2pekC 2pemC 2peoC 2peqC C: citing same article (ref.)
Similar structure data	2pej-1 2z46-1 2pem-2 2z46-2 2pei-4 2peq-d 2pei-6 4v3q-4 2pek-2 2pei-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: ORF134

B: ORF134

C: ORF134

D: ORF134

E: ORF134

F: ORF134

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

1

A: ORF134

B: ORF134

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

2

C: ORF134

D: ORF134

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

3

E: ORF134

F: ORF134

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

4

C: ORF134

D: ORF134

E: ORF134

F: ORF134

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

Unit cell

Length a, b, c (Å)	93.335, 93.335, 411.990
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Details

The biological unit is a dimer. There are 3 biological units in the asymmetric unit (chains A & B, chains C & D and chains E & F).

#1: Protein	ORF134 Mass: 15284.084 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: RbcX / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q44177
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

ORF134

Mass: 15284.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: RbcX / Plasmid: pET11a / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q44177

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.89 Å³/Da / Density % sol: 74.85 % Description: Data collected at ESRF BEAMLINE BM14 using wavelength 0.8793 A was for Pt derivative
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.30-1.55 M Sodium acetate, 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SLS	X10SA	1	0.9789
SYNCHROTRON	ESRF	BM14	2	0.8793

Detector

Type	ID	Detector	Date
MARMOSAIC 225 mm CCD	1	CCD	Jun 18, 2005
MARMOSAIC 225 mm CCD	2	CCD	Jun 30, 2005

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9789	1
2	0.8793	1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	Num. obs	% possible obs
7	1	4.3	229045	0.081	0.081	3.15	102.062	32533	100
7.4	2	6	337895	0.078	0.078	2.8	102.598	45745	99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
9.96	93.25	99.4	1	0.036	0.036	5.7
7.04	9.96	99.9	1	0.036	0.036	6.6
5.75	7.04	100	1	0.061	0.061	6.9
4.98	5.75	100	1	0.067	0.067	7
4.45	4.98	100	1	0.061	0.061	7.1
4.07	4.45	100	1	0.074	0.074	7.1
3.76	4.07	100	1	0.125	0.125	7.2
3.52	3.76	100	1	0.194	0.194	7.2
3.32	3.52	100	1	0.334	0.334	7.2
3.15	3.32	100	1	0.621	0.621	7.2
8.85	93.66	99.5	2	0.029	0.029	6.1
6.26	8.85	99.6	2	0.039	0.039	7
5.11	6.26	99.5	2	0.054	0.054	7.2
4.43	5.11	99.3	2	0.047	0.047	7.3
3.96	4.43	99.3	2	0.056	0.056	7.4
3.61	3.96	99.1	2	0.088	0.088	7.5
3.35	3.61	99.1	2	0.147	0.147	7.5
3.13	3.35	98.9	2	0.299	0.299	7.5
2.95	3.13	98.9	2	0.546	0.546	7.6
2.8	2.95	98.7	2	0.864	0.864	7.6

Reflection

Resolution: 2.8→411.99 Å / Num. obs: 46362 / % possible obs: 100 % / Redundancy: 14.5 % / R_merge(I) obs: 0.08 / R_sym value: 0.08 / Net I/σ(I): 6.5

Reflection shell

Diffraction-ID: 1,2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.8-2.95	14.8	0.641	1.2	98241	6617	0.641	100
2.95-3.13	14.8	0.423	1.8	93231	6285	0.423	100
3.13-3.35	14.8	0.239	3.1	87686	5926	0.239	100
3.35-3.61	14.8	0.127	5.7	81291	5508	0.127	100
3.61-3.96	14.7	0.083	8.2	75012	5106	0.083	100
3.96-4.43	14.6	0.059	10.7	68455	4688	0.059	100
4.43-5.11	14.4	0.061	9.1	59828	4143	0.061	100
5.11-6.26	14.2	0.081	7.1	50847	3573	0.081	100
6.26-8.85	13.8	0.053	10.1	39081	2822	0.053	100
8.85-91.03	12.1	0.036	14.8	20522	1694	0.036	99.2

-
Phasing

Phasing

Method:

SIRAS

Phasing dm

FOM : 0.4 / FOM acentric: 0.43 / FOM centric: 0.36 / Reflection: 1067 / Reflection acentric: 641 / Reflection centric: 426

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8-24.834	0.4	0.43	0.36	1067	641	426
5-8
4-5
3.5-4
3-3.5
2.8-3

Phasing MIR der

ID	Der set-ID
1	1
2	1
3	1
4	1
5	1
6	1

Phasing MIR der site

ID: 1 / B_iso : 60 Å / Atom type symbol: Pt

Der-ID	Fract x	Fract y	Fract z	Occupancy
1	0.7326	0.9921	0.0955	0.357
2	0.0597	0.0897	0.1214	0.3104
3	0.2027	0.1864	0.0812	0.37
4	0.5221	0.0734	0.0701	0.3047
5	0.0521	0.5536	0.0045	0.2283
6	0.2455	0.4467	0.0312	0.2888

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
SOLVE	2.01	phasing
RESOLVE	2.01	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
MAR345	CCD	data collection
MOSFLM		data reduction

Refinement

Method to determine structure:

SIRAS / Resolution: 2.8→20 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.91 / SU B: 9.742 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.262	2321	5 %	RANDOM
R_work	0.24	-	-	-
obs	0.242	46068	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 64.684 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.29 Å²	0 Å²	0 Å²
2-	-	0.29 Å²	0 Å²
3-	-	-	-0.57 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5086	0	0	19	5105

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	5158
X-RAY DIFFRACTION	r_angle_refined_deg	1.406	1.978	6994
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.226	5	651
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.808	24.336	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.646	15	908
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.845	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	839
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3803
X-RAY DIFFRACTION	r_nbd_refined	0.244	0.2	2483
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	3589
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.108	0.2	144
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.203	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.019	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.694	1.5	3352
X-RAY DIFFRACTION	r_mcangle_it	1.279	2	5219
X-RAY DIFFRACTION	r_scbond_it	1.788	3	1997
X-RAY DIFFRACTION	r_scangle_it	3.081	4.5	1775

LS refinement shell

Resolution: 2.8→2.871 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	167	-
R_work	0.354	3123	-
obs	-	3290	100 %

-
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