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- PDB-4hhh: Structure of Pisum sativum Rubisco -

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Basic information

Entry
Database: PDB / ID: 4hhh
TitleStructure of Pisum sativum Rubisco
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small chain
KeywordsLYASE / rubisco / ribulose-1 / 5-bisphosphate
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 3
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLoewen, P.C. / Didychuk, A.L. / Switala, J. / Loewen, M.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of Pisum sativum Rubisco with bound ribulose 1,5-bisphosphate.
Authors: Loewen, P.C. / Didychuk, A.L. / Switala, J. / Perez-Luque, R. / Fita, I. / Loewen, M.C.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain
T: Ribulose bisphosphate carboxylase small chain
U: Ribulose bisphosphate carboxylase small chain
V: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,36912
Polymers270,1288
Non-polymers1,2404
Water14,214789
1
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain
T: Ribulose bisphosphate carboxylase small chain
U: Ribulose bisphosphate carboxylase small chain
V: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain
T: Ribulose bisphosphate carboxylase small chain
U: Ribulose bisphosphate carboxylase small chain
V: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,73724
Polymers540,25716
Non-polymers2,4818
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area111960 Å2
ΔGint-448 kcal/mol
Surface area118930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.790, 109.950, 201.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17S
27T
18S
28U
19S
29V
110T
210U
111T
211V
112U
212V

NCS domain segments:

Refine code: _

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPHEPHEAA12 - 46912 - 469
221GLYGLYPHEPHEBB12 - 46912 - 469
112GLYGLYPHEPHEAA12 - 46912 - 469
222GLYGLYPHEPHECC12 - 46912 - 469
113GLYGLYPHEPHEAA12 - 46912 - 469
223GLYGLYPHEPHEDD12 - 46912 - 469
114GLYGLYPHEPHEBB12 - 46912 - 469
224GLYGLYPHEPHECC12 - 46912 - 469
115GLYGLYPHEPHEBB12 - 46912 - 469
225GLYGLYPHEPHEDD12 - 46912 - 469
116GLYGLYPHEPHECC12 - 46912 - 469
226GLYGLYPHEPHEDD12 - 46912 - 469
117METMETTYRTYRSE1 - 1231 - 123
227METMETTYRTYRTF1 - 1231 - 123
118METMETTYRTYRSE1 - 1231 - 123
228METMETTYRTYRUG1 - 1231 - 123
119METMETTYRTYRSE1 - 1231 - 123
229METMETTYRTYRVH1 - 1231 - 123
1110METMETTYRTYRTF1 - 1231 - 123
2210METMETTYRTYRUG1 - 1231 - 123
1111METMETTYRTYRTF1 - 1231 - 123
2211METMETTYRTYRVH1 - 1231 - 123
1112METMETTYRTYRUG1 - 1231 - 123
2212METMETTYRTYRVH1 - 1231 - 123

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52831.992 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Tissue: leaf
References: UniProt: P04717, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain


Mass: 14700.099 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Tissue: leaf / References: UniProt: P07689*PLUS
#3: Sugar
ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG6000, 0.1 M HEPES, pH 7.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: Marmosaic / Detector: CCD / Date: Aug 10, 2011 / Details: mirrors
RadiationMonochromator: Double crystal SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.58
11K, H, -L20.42
ReflectionResolution: 2.2→109.95 Å / Num. all: 116075 / Num. obs: 116075 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.222 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.322.60.3871.744423170840.38795.5
2.32-2.462.70.341.942855161410.3495.4
2.46-2.632.70.3012.240589151190.30195
2.63-2.842.70.2662.538150140200.26694.5
2.84-3.112.80.2272.935454128630.22793.8
3.11-3.482.80.2043.232287116120.20493.7
3.48-4.022.80.183.528662102520.1893.3
4.02-4.922.80.1653.82433086450.16592.7
4.92-6.962.80.1633.51876466770.16391.7
6.96-48.2012.80.1473.11008836620.14789.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CLSIdata collection
MOSFLMdata reduction
PHENIXMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→109.95 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.734 / WRfactor Rfree: 0.2931 / WRfactor Rwork: 0.2034 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8398 / SU B: 4.102 / SU ML: 0.108 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0573 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 5993 5.2 %RANDOM
Rwork0.1972 ---
all0.2014 110030 --
obs0.2014 116023 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.33 Å2 / Biso mean: 10.6478 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--6.73 Å2-0 Å2-0 Å2
2--0.84 Å20 Å2
3---5.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→109.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18528 0 72 789 19389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0219441
X-RAY DIFFRACTIONr_angle_refined_deg2.4461.95826445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.03552424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75722.925906
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.867153245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.36315154
X-RAY DIFFRACTIONr_chiral_restr0.160.22812
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02114996
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A5530.23
12B5530.23
21A5510.21
22C5510.21
31A5600.23
32D5600.23
41B5580.22
42C5580.22
51B5540.22
52D5540.22
61C5500.23
62D5500.23
71S1090.14
72T1090.14
81S1130.15
82U1130.15
91S1130.15
92V1130.15
101T1140.15
102U1140.15
111T1100.14
112V1100.14
121U1140.15
122V1140.15
LS refinement shellResolution: 2.2→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 414 -
Rwork0.195 7714 -
all-8128 -
obs--89.06 %

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