[English] 日本語
Yorodumi
- PDB-2wwr: Crystal Structure of Human Glyoxylate Reductase Hydroxypyruvate R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wwr
TitleCrystal Structure of Human Glyoxylate Reductase Hydroxypyruvate Reductase
ComponentsGLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
KeywordsOXIDOREDUCTASE / MOLECULAR CONFORMATION
Function / homology
Function and homology information


dicarboxylic acid metabolic process / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / glyoxylate metabolic process / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process ...dicarboxylic acid metabolic process / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / glyoxylate metabolic process / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process / peroxisomal matrix / catalytic complex / NADPH binding / NAD binding / protein homodimerization activity / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyoxylate reductase/hydroxypyruvate reductase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsBooth, M.P.S. / Conners, R. / Rumsby, G. / Brady, R.L.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of Substrate Specificity in Human Glyoxylate Reductase/Hydroxypyruvate Reductase.
Authors: Booth, M.P. / Conners, R. / Rumsby, G. / Brady, R.L.
History
DepositionOct 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
B: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
C: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
D: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,5266
Polymers143,4774
Non-polymers492
Water84747
1
C: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
D: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7633
Polymers71,7392
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-46.7 kcal/mol
Surface area26550 Å2
MethodPISA
2
A: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
B: GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7633
Polymers71,7392
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-41 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.356, 116.080, 198.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUHISHISBB45 - 5347 - 55
21LEULEUHISHISDD45 - 5347 - 55
12ASPASPASNASNBB61 - 7463 - 76
22ASPASPASNASNDD61 - 7463 - 76
13LEULEUGLUGLUBB88 - 9290 - 94
23LEULEUGLUGLUDD88 - 9290 - 94
14ARGARGVALVALBB96 - 10098 - 102
24ARGARGVALVALDD96 - 10098 - 102

NCS oper:
IDCodeMatrixVector
1given(-0.7202, 0.5409, -0.4346), (0.5091, -0.01358, -0.8606), (-0.4714, -0.841, -0.2656)-54.09, -30.53, -68.94
2given(1, 0.007176, -0.001939), (0.007185, -1, 0.004512), (-0.001907, -0.004526, -1)33.61, 0.05581, -51
3given(-0.7025, 0.5101, -0.4963), (-0.5622, 0.02981, 0.8265), (0.4364, 0.8596, 0.2658)-23.14, 27.67, 17.15

-
Components

#1: Protein
GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE


Mass: 35869.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRCHISB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9UBQ7, glyoxylate reductase (NADP+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES IN CHAIN SEQUENCE ARE CLONING ARTIFACTS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 % / Description: NONE
Crystal growDetails: 0.1M SODIUM CACODYLATE PH 6.75, 10% PEG 8K, 0.25M MAGNESIUM ACETATE TETRAHYDRATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.95
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 34609 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.5
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GCG
Resolution: 2.82→100 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 31.778 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27857 1737 5 %RANDOM
Rwork0.21739 ---
obs0.22036 32826 90.63 %-
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: 36.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--3.55 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.82→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9591 0 2 47 9640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.97712814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09651230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05524.011359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.202151521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9691562
X-RAY DIFFRACTIONr_chiral_restr0.0690.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027004
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.23930
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.26378
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2421.56354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43329881
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.53633443
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9034.52933
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

Ens-ID: 1 / Number: 135 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Btight positional0.030.05
2Dtight positional0.030.05
1Btight thermal0.370.5
2Dtight thermal0.370.5
LS refinement shellResolution: 2.82→2.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 147 -
Rwork0.262 2126 -
obs--82.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.4765-2.2534-0.542311.876-1.0950.1631-0.1831-0.34750.07540.6351-0.0855-0.4326-0.32920.12710.26860.263-0.0259-0.03190.15390.0468-0.0043-38.917321.9335-30.6182
24.04161.8021-0.21824.9783-0.05130.26630.1453-0.49940.35230.3424-0.05770.1979-0.22360.009-0.08750.2095-0.00650.03920.1615-0.02870.1412-44.350518.6201-29.0255
32.4922-1.83650.00431.9960.3090.1517-0.00670.08980.0504-0.0286-0.03090.0381-0.0268-0.04720.03750.1895-0.01920.02750.09250.02280.1902-38.807313.1161-44.0662
42.5377-1.38050.55613.4251-1.02041.45010.08840.211-0.2449-0.41830.02820.31030.2551-0.0384-0.11660.1163-0.0699-0.04240.073-0.06960.1651-18.2816-6.3802-54.2615
52.79150.68980.651.21180.41270.21240.03960.31540.2728-0.72180.1108-0.1056-0.06440.2592-0.15040.28970.0012-0.05010.12220.04860.1162-20.67178.5808-61.0647
66.45013.42882.170111.07130.49272.8739-0.32970.66330.537-1.28310.44570.8666-0.2479-0.2197-0.1160.22960.0133-0.15470.10510.08790.0958-29.27328.1835-65.8602
74.0991-0.68893.81670.1238-0.94214.76990.09870.5164-0.0684-0.1919-0.24730.29670.4197-0.14250.14860.1998-0.0308-0.19120.0309-0.0830.368-33.7128-6.4511-63.2847
83.86950.5754-1.68471.2092-0.2823.7620.0222-0.0544-0.3717-0.0931-0.07630.43870.2049-0.33650.05410.1304-0.0568-0.06640.0213-0.00070.3406-36.4806-5.5842-50.7131
91.922-3.4058-1.08411.68152.30341.53410.0577-0.15090.11790.1185-0.0288-0.2345-0.17770.3375-0.02890.1137-0.03930.04480.10970.06450.2405-31.29715.5578-40.2147
109.3451-2.3507-1.76016.58410.67759.9301-0.59070.44610.9195-0.24740.32970.2072-0.71650.97350.2610.1817-0.0387-0.0032-0.06140.04240.2418-40.021531.1565-44.3636
114.79850.12770.49165.7833-1.54576.50040.01830.2131-0.3905-0.33340.0443-0.13050.8342-0.235-0.06260.1772-0.02120.08930.06-0.01960.1188-2.5384-24.7115-63.2581
124.50553.9215-5.06264.8348-1.434611.9005-0.27450.5951-0.089-0.3641-0.0931-0.06880.3547-0.15780.36760.10890.11140.0450.0608-0.00150.1797-1.7846-29.0201-56.5639
136.01080.22361.19319.19371.33632.750.4943-0.5082-0.26320.4548-0.2755-0.58360.21810.5792-0.21880.0210.0853-0.0213-0.03340.04520.1538.1516-26.1807-53.1534
142.7111-4.02591.95575.9808-2.83853.2534-0.2187-0.5181-0.73220.5682-0.2655-0.0778-0.9693-0.5520.48420.0538-0.03830.02320.0391-0.02640.16074.0869-14.6664-54.6181
156.43563.3412-2.08332.148-0.42631.7133-0.1694-0.75110.1288-0.15640.0228-0.9672-0.2890.42720.1465-0.04220.06070.02640.0043-0.06340.154910.6275-14.409-55.1041
164.03240.38430.85250.51470.75741.13660.3463-0.0822-0.0948-0.3476-0.32040.0687-0.74250.1064-0.02590.23410.0270.00220.00470.03440.2868-13.94180.2735-47.8681
172.8474-0.50210.93390.83190.00920.35430.02670.0031-0.03030.103-0.11480.0305-0.1063-0.06790.08810.1529-0.00940.02870.0708-0.00280.1721-19.59944.9335-42.5194
183.00080.36092.4443.8681-4.35528.14140.131-0.06830.04960.0309-0.3567-0.4194-0.08440.62350.22570.08230.0007-0.00050.0666-0.0110.2313-1.697810.0518-42.0948
190.4225-0.102-0.54671.0770.23981.0698-0.0136-0.0455-0.05350.044-0.0007-0.1168-0.01430.00050.01430.1740.0094-0.01620.11210.01420.2451-7.4395-8.145-42.7308
2010.7244-4.30342.35781.7268-0.94610.5184-0.0672-0.49511.1468-0.7396-0.0457-1.60490.19430.0570.11290.1389-0.16510.21380.2326-0.01910.61529.8588-11.5409-64.7177
213.7001-4.74991.90216.823-1.17085.16650.51060.3292-0.227-0.8424-0.4114-0.14371.15450.3856-0.09910.35410.0194-0.04310.05720.04620.0308-5.9605-23.124-21.7397
228.381.2874-1.85554.2784-3.40572.7974-0.0292-0.21280.1897-0.27020.27880.56210.2785-0.4144-0.24960.198-0.0718-0.04640.1120.03510.0751-15.7031-18.4155-14.7233
233.77823.59370.42174.10020.03160.55880.2697-0.38160.09670.3877-0.05840.36980.1647-0.1514-0.21130.17610.03180.08340.22020.09280.11970.8787-9.7264-3.7889
240.56860.7136-1.1024.9041-2.42395.3089-0.0778-0.2990.22130.72660.22660.33770.08720.3799-0.14880.17790.1320.04550.1917-0.0003-0.015215.72156.74563.3
251.908-0.73161.63394.61141.7242.6747-0.41950.3541-0.41451.86830.85190.42780.46690.2728-0.43230.56350.05980.07320.14450.0403-0.056314.765-9.30817.9449
262.7349-3.5670.22086.49521.62051.9939-0.3069-0.8386-0.26741.49090.29361.03710.5227-0.50580.01330.64430.00430.37190.32010.1136-0.04593.6565-4.493614.3696
274.69231.9174-3.13450.7949-1.46955.2228-0.1491-0.64710.08750.7392-0.1172.0098-0.0166-0.27220.26610.2124-0.00840.30270.11-0.09090.3689-4.0162.99583.353
283.11831.84163.17396.31412.26254.78950.0964-0.03350.12660.3673-0.0250.8315-0.0876-0.1128-0.0714-0.00150.01810.16510.1517-0.00380.3553-2.15286.8189-2.5358
291.36034.27371.478918.46082.99892.1470.1275-0.03790.0938-0.0799-0.08870.2510.39270.0474-0.03880.19470.0530.00660.11610.1390.17252.5944-14.8598-10.2877
3010.6064-1.765-1.92858.343-5.1064.00950.6355-1.4693-1.58750.2759-0.07050.1771.54790.395-0.5650.4001-0.1526-0.21440.4730.15380.3359-6.2876-31.6022-6.3765
3110.25481.44367.46590.36682.556719.2977-1.21110.70030.6953-0.1940.27830.1221-1.4091.52280.93270.2766-0.1474-0.14160.24390.10290.002731.111925.083913.7807
3221.62318.18145.982315.95877.05517.7656-1.93510.39691.00080.19110.45040.1069-2.0343-1.89031.48470.34820.0279-0.40330.41360.33380.351629.459329.71863.93
3329.199314.6716-6.87199.715-10.641223.67120.56361.1130.94780.9813-0.9464-0.1499-2.02581.88360.38280.2739-0.2401-0.22220.34740.22380.339938.646226.47663.8139
3422.52244.7928-11.83352.9314-1.524420.48750.07160.5743-0.2255-0.55370.0262-0.32940.90041.6432-0.09770.13430.0702-0.15970.6621-0.0735-0.057141.165215.32054.2258
356.54931.20412.03861.672-0.17180.8406-0.0607-0.21140.51490.2406-0.07040.22610.2617-0.16660.1310.1740.02570.01670.30780.03030.142410.4594-2.1663-9.5306
362.90661.9981-1.51673.1134-3.45394.13340.0108-0.2297-0.12920.584-0.0338-0.38020.06820.07250.0230.19360.03-0.07420.25990.07560.060427.3817-10.2317-1.9854
371.08231.7443-2.2913.724-2.147.48940.1314-0.4401-0.22660.513-0.2521-1.01570.28490.87710.12070.13310.0773-0.12810.14840.11360.2934.0838-9.9395-7.8443
380.9415-0.786-0.51773.0853-1.63732.04770.006-0.10460.0429-0.1068-0.0257-0.1121-0.0292-0.01490.01980.11420.00890.01510.18280.03130.162724.96143.4161-16.9984
395.42165.28695.96885.74354.286210.57540.6522-0.1725-0.6060.1862-0.2124-0.16760.55730.5859-0.43990.20680.0841-0.05490.4102-0.11270.080428.922813.977311.0188
4016.3128-3.578916.64570.7883-3.622317.26411.2642-0.7315-2.1177-0.06550.5554-1.54390.97951.1536-1.81960.3914-0.0695-0.05790.3951-0.08340.376642.277915.634816.6723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 22
2X-RAY DIFFRACTION2A23 - 48
3X-RAY DIFFRACTION3A49 - 134
4X-RAY DIFFRACTION4A135 - 164
5X-RAY DIFFRACTION5A165 - 182
6X-RAY DIFFRACTION6A183 - 225
7X-RAY DIFFRACTION7A226 - 239
8X-RAY DIFFRACTION8A240 - 287
9X-RAY DIFFRACTION9A288 - 316
10X-RAY DIFFRACTION10A317 - 327
11X-RAY DIFFRACTION11B6 - 25
12X-RAY DIFFRACTION12B26 - 43
13X-RAY DIFFRACTION13B44 - 76
14X-RAY DIFFRACTION14B77 - 86
15X-RAY DIFFRACTION15B87 - 106
16X-RAY DIFFRACTION16B107 - 125
17X-RAY DIFFRACTION17B126 - 173
18X-RAY DIFFRACTION18B174 - 235
19X-RAY DIFFRACTION19B236 - 318
20X-RAY DIFFRACTION20B319 - 327
21X-RAY DIFFRACTION21C6 - 36
22X-RAY DIFFRACTION22C37 - 80
23X-RAY DIFFRACTION23C81 - 134
24X-RAY DIFFRACTION24C135 - 164
25X-RAY DIFFRACTION25C165 - 179
26X-RAY DIFFRACTION26C180 - 239
27X-RAY DIFFRACTION27C240 - 258
28X-RAY DIFFRACTION28C259 - 286
29X-RAY DIFFRACTION29C287 - 316
30X-RAY DIFFRACTION30C317 - 327
31X-RAY DIFFRACTION31D6 - 28
32X-RAY DIFFRACTION32D29 - 43
33X-RAY DIFFRACTION33D44 - 76
34X-RAY DIFFRACTION34D77 - 106
35X-RAY DIFFRACTION35D107 - 152
36X-RAY DIFFRACTION36D153 - 182
37X-RAY DIFFRACTION37D183 - 228
38X-RAY DIFFRACTION38D229 - 294
39X-RAY DIFFRACTION39D295 - 316
40X-RAY DIFFRACTION40D317 - 325

+
About Yorodumi

-
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://pdbjlvh1.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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more