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- PDB-1uzh: A CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME -

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Basic information

Entry
Database: PDB / ID: 1uzh
TitleA CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME
Components(RIBULOSE BISPHOSPHATE CARBOXYLASE ...RuBisCO) x 2
KeywordsLYASE / RUBISCO / PHOTOSYNTHESIS / CARBON DIOXIDE FIXATION / PHOTORESPIRATION / OXIDOREDUCTASE / MONOOXYGENASE / CHLOROPLAST / TRANSIT PEPTIDE / MULTIGENE FAMILY
Function / homology
Function and homology information


photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
SYNECHOCOCCUS SP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarkehabadi, S. / Spreitzer, R.J. / Andersson, I.
CitationJournal: Biochemistry / Year: 2005
Title: Chimeric Small Subunits Influence Catalysis without Causing Global Conformational Changes in the Crystal Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase
Authors: Karkehabadi, S. / Peddi, S.R. / Anwaruzzaman, M. / Taylor, T.C. / Cederlund, A. / Genkov, T. / Andersson, I. / Spreitzer, R.J.
History
DepositionMar 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 18, 2019Group: Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_database_status
Item: _entity.src_method / _pdbx_database_status.status_code_sf
Revision 1.5Jul 29, 2020Group: Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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

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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 SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
F: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
H: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
J: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
K: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
M: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
O: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
P: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
R: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
T: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
V: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
W: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,10282
Polymers535,95516
Non-polymers6,14766
Water51,0002831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)220.820, 223.969, 111.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41H
51K
61O
71R
81V
12I
22C
32F
42J
52P
62T
72M
82W

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA12 - 47512 - 475
21GLYGLYLEULEUBB12 - 47512 - 475
31GLYGLYLEULEUED12 - 47512 - 475
41GLYGLYLEULEUHF12 - 47512 - 475
51GLYGLYLEULEUKI12 - 47512 - 475
61GLYGLYLEULEUOK12 - 47512 - 475
71GLYGLYLEULEURM12 - 47512 - 475
81GLYGLYLEULEUVO12 - 47512 - 475
12METMETVALVALIG1 - 1221 - 122
22METMETVALVALCC1 - 1221 - 122
32METMETVALVALFE1 - 1221 - 122
42METMETVALVALJH1 - 1221 - 122
52METMETVALVALPL1 - 1221 - 122
62METMETVALVALTN1 - 1221 - 122
72METMETVALVALMJ1 - 1221 - 122
82METMETVALVALWP1 - 1221 - 122

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.9501, 0.303, 0.07433), (0.3029, -0.9529, 0.01175), (0.07439, 0.01136, -0.9972)-12.68, 68.85, 51.71
2given(-0.3024, 0.9532, 0.001929), (0.9532, 0.3024, 0.001161), (0.000523, 0.002189, -1)41.8, -30.84, 57.09
3given(-0.9534, -0.3014, 0.01301), (-0.3016, 0.9508, -0.07126), (0.009109, -0.07186, -0.9974)141.60001, 23.96, 59.81
4given(0.000223, 0.9973, -0.07319), (-0.9999, -0.000675, -0.01224), (-0.01226, 0.07319, 0.9972)22.08, 111.6, -2.458
5given(0.007167, -0.9999, -0.01476), (0.9975, 0.006105, 0.07081), (-0.07071, -0.01523, 0.9974)111.2, -22.26, 5.478
6given(-0.9966, -0.003438, -0.08292), (-0.001574, -0.9982, 0.0603), (-0.08298, 0.06022, 0.9947)133.5, 89.63, 2.841
7given(0.3034, -0.9493, 0.08198), (-0.9493, -0.3086, -0.0604), (0.08264, -0.05949, -0.9948)86.64, 123.8, 54.3
8given(0.9484, 0.3076, 0.07617), (0.3079, -0.9514, 0.008797), (0.07517, 0.01511, -0.9971)-12.83, 68.61, 51.54
9given(-0.3064, 0.9519, 0.001248), (0.9519, 0.3064, 4.4E-5), (-0.00034, 0.001202, -1)42.11, -30.79, 57.17
10given(-0.952, -0.3056, 0.01431), (-0.3058, 0.9491, -0.07475), (0.009259, -0.07554, -0.9971)141.7, 24.46, 59.98
11given(0.003915, 0.9972, -0.07474), (-1, 0.003271, -0.008736), (-0.008467, 0.007478, 0.9972)21.9, 111.3, -2.749
12given(-0.000288, -0.9999, -0.01538), (0.9972, -0.001435, 0.07465), (-0.07466, -0.01531, 0.9971)111.7, -21.88, 5.743
13given(-0.9967, -0.002425, -0.08124), (-0.002427, -0.9982, 0.05957), (-0.08124, 0.05957, 0.9949)133.39999, 89.75, 2.764
14given(0.3028, -0.9493, 0.08405), (-0.9496, -0.308, -0.05807), (0.08101, -0.06223, -0.9948)86.72, 123.8, 54.66
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

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Components

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RIBULOSE BISPHOSPHATE CARBOXYLASE ... , 2 types, 16 molecules ABEHKORVCFIJMPTW

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RUBISCO LARGE SUBUNIT / RIBULOSE-1 / 5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN


Mass: 52696.840 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant), (gene. exp.) SYNECHOCOCCUS SP (bacteria)
Production host: SYNECHOCOCCUS SP (bacteria)
References: UniProt: P00877, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN / RUBISCO SMALL SUBUNIT 1 / CHLOROPLAST / RUBISCO SMALL SUBUNIT 2 / OXYGENASE / RIBULOSE-1 / 5 ...RUBISCO SMALL SUBUNIT 1 / CHLOROPLAST / RUBISCO SMALL SUBUNIT 2 / OXYGENASE / RIBULOSE-1 / 5 BISPHOSPHATE CARBOXYLASE/OXYGENASE


Mass: 14297.542 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: LOOP BA-BB OF SMALL SUBUNIT CHLAMYDOMONAS RUBISCO, RESIDUES E47 - R71 HAS BEEN REPLACED WITH THE CORRESPONDING LOOP OF SYNECHOCOCCUSS, RESIDUES H47 - F53
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: CHLAMYDOMONAS REINHARDTII (plant)
References: UniProt: P00873, UniProt: P04716, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 8 molecules

#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 2889 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Source: (gene. exp.) SYNECHOCOCCUS SP (bacteria) / Production host: SYNECHOCOCCUS SP (bacteria)
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2831 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRUBISCO CATALYZES TWO REACTIONS: THE CARBOXYLATION OF D- RIBULOSE 1,5-BISPHOSPHATE, THE PRIMARY ...RUBISCO CATALYZES TWO REACTIONS: THE CARBOXYLATION OF D- RIBULOSE 1,5-BISPHOSPHATE, THE PRIMARY EVENT IN PHOTOSYNTHETIC CARBON DIOXIDE FIXATION, AS WELL AS THE OXIDATIVE FRAGMENTATION OF THE PENTOSE SUBSTRATE IN THE PHOTORESPIRATION PROCESS. BOTH REACTIONS OCCUR SIMULTANEOUSLY AND IN COMPETITION AT THE SAME ACTIVE SITE.
Sequence detailsLOOP BA-BB OF SMALL SUBUNIT CHLAMYDOMONAS RUBISCO, RESIDUES 47 - 71 (ADKAYVSNESAIRFGSVSCLYYDNR) HAS ...LOOP BA-BB OF SMALL SUBUNIT CHLAMYDOMONAS RUBISCO, RESIDUES 47 - 71 (ADKAYVSNESAIRFGSVSCLYYDNR) HAS BEEN REPLACED WITH THE CORRESPONDING LOOP OF SYNECHOCOCCUSS RUBISCO, RESIDUES 47 - 53 (HSNPEEF). SINCE THIS LOOP IN RUBISCO FROM SYNECHOCOCCUSS IS SMALLER, THE NUMBERING OF THE SMALL SUBUNIT IN THE COORDINATE FILE HAS BEEN CHANGED IN ORDER TO BE CONSEQUTIVE.

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 50 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 277345 / % possible obs: 90.2 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 8.65
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / % possible all: 81.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GK8

1gk8


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.913 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.193 12557 5 %RANDOM
Rwork0.16 ---
obs0.162 237038 89.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.94 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37215 0 376 2831 40422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02138620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.95252270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88954706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.25536
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0229648
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.219454
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.23178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.084323472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.007537683
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.142615148
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.394814585
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3603tight positional0.040.05
12B3603tight positional0.040.05
13E3603tight positional0.040.05
14H3603tight positional0.040.05
15K3603tight positional0.040.05
16O3603tight positional0.040.05
17R3603tight positional0.040.05
18V3603tight positional0.040.05
21I989tight positional0.030.05
22C989tight positional0.030.05
23F989tight positional0.040.05
24J989tight positional0.030.05
25P989tight positional0.030.05
26T989tight positional0.040.05
27M989tight positional0.040.05
28W989tight positional0.040.05
11A3603tight thermal0.140.5
12B3603tight thermal0.140.5
13E3603tight thermal0.140.5
14H3603tight thermal0.150.5
15K3603tight thermal0.140.5
16O3603tight thermal0.140.5
17R3603tight thermal0.140.5
18V3603tight thermal0.150.5
21I989tight thermal0.110.5
22C989tight thermal0.110.5
23F989tight thermal0.110.5
24J989tight thermal0.120.5
25P989tight thermal0.110.5
26T989tight thermal0.120.5
27M989tight thermal0.110.5
28W989tight thermal0.130.5
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 679
Rwork0.212 13878

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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