[English] 日本語
Yorodumi
- PDB-4kws: Crystal structure of d-mannonate dehydratase from chromohalobacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kws
TitleCrystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg and glycerol
ComponentsD-mannonate dehydratase
KeywordsHYDROLASE / enolase fold / D-MANNONATE DEHYDRATASE
Function / homology
Function and homology information


gluconate dehydratase / gluconate dehydratase activity / mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-galactonate dehydratase family member ManD
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.642 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg and glycerol
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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.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_ref_seq_dif.details / _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: D-mannonate dehydratase
B: D-mannonate dehydratase
C: D-mannonate dehydratase
D: D-mannonate dehydratase
E: D-mannonate dehydratase
F: D-mannonate dehydratase
G: D-mannonate dehydratase
H: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,94133
Polymers363,7468
Non-polymers1,19525
Water53,1982953
1
A: D-mannonate dehydratase
B: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2539
Polymers90,9372
Non-polymers3177
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-31 kcal/mol
Surface area26300 Å2
MethodPISA
2
C: D-mannonate dehydratase
D: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,27810
Polymers90,9372
Non-polymers3418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-42 kcal/mol
Surface area26450 Å2
MethodPISA
3
E: D-mannonate dehydratase
H: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2057
Polymers90,9372
Non-polymers2685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-33 kcal/mol
Surface area26390 Å2
MethodPISA
4
F: D-mannonate dehydratase
G: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2057
Polymers90,9372
Non-polymers2685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-34 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.273, 85.762, 195.097
Angle α, β, γ (deg.)90.00, 110.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

MG

21B-503-

MG

31C-504-

MG

41D-503-

MG

51A-968-

HOH

61E-980-

HOH

-
Components

#1: Protein
D-mannonate dehydratase


Mass: 45468.258 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_2974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QT89, mannonate dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2953 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG 3350, 0.1M Succinic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.642→40.047 Å / Num. all: 366760 / Num. obs: 366760 / % possible obs: 99.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OW1

3ow1


Resolution: 1.642→40.047 Å / SU ML: 0.13 / σ(F): 1.33 / Phase error: 15.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1625 18482 5.04 %
Rwork0.1385 --
obs0.1397 348304 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4309 Å2-0 Å2-0.4854 Å2
2---1.5663 Å2-0 Å2
3----1.8646 Å2
Refinement stepCycle: LAST / Resolution: 1.642→40.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25040 0 65 2953 28058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625972
X-RAY DIFFRACTIONf_angle_d1.08535407
X-RAY DIFFRACTIONf_dihedral_angle_d12.6629324
X-RAY DIFFRACTIONf_chiral_restr0.0763819
X-RAY DIFFRACTIONf_plane_restr0.0054624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6423-1.6610.22855560.184111255X-RAY DIFFRACTION97
1.661-1.68050.19816450.165111594X-RAY DIFFRACTION100
1.6805-1.7010.20336230.166111531X-RAY DIFFRACTION100
1.701-1.72250.20366100.166211582X-RAY DIFFRACTION100
1.7225-1.74520.20496160.159211643X-RAY DIFFRACTION100
1.7452-1.76910.20026260.160911461X-RAY DIFFRACTION100
1.7691-1.79440.19996110.164311636X-RAY DIFFRACTION100
1.7944-1.82120.19855880.153611560X-RAY DIFFRACTION100
1.8212-1.84960.19716320.148311539X-RAY DIFFRACTION100
1.8496-1.880.17746260.144211594X-RAY DIFFRACTION100
1.88-1.91240.16866660.140111571X-RAY DIFFRACTION100
1.9124-1.94710.18036100.147111583X-RAY DIFFRACTION100
1.9471-1.98460.1846670.147111532X-RAY DIFFRACTION100
1.9846-2.02510.18076110.145311554X-RAY DIFFRACTION100
2.0251-2.06910.16565770.136511657X-RAY DIFFRACTION100
2.0691-2.11730.16826130.132511574X-RAY DIFFRACTION100
2.1173-2.17020.17385980.136811634X-RAY DIFFRACTION100
2.1702-2.22890.17196410.136111567X-RAY DIFFRACTION100
2.2289-2.29450.1616330.131211622X-RAY DIFFRACTION100
2.2945-2.36850.16426400.134711632X-RAY DIFFRACTION100
2.3685-2.45320.16916000.141711646X-RAY DIFFRACTION100
2.4532-2.55140.17055700.134711619X-RAY DIFFRACTION100
2.5514-2.66750.16675910.143611722X-RAY DIFFRACTION100
2.6675-2.80810.16296050.140411634X-RAY DIFFRACTION100
2.8081-2.98390.16195800.144511701X-RAY DIFFRACTION100
2.9839-3.21420.16575900.144611670X-RAY DIFFRACTION100
3.2142-3.53750.15236370.135211686X-RAY DIFFRACTION100
3.5375-4.0490.1296320.121711715X-RAY DIFFRACTION100
4.049-5.09970.12396030.114211782X-RAY DIFFRACTION100
5.0997-40.05870.1576850.145811785X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°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)
10.2982-0.05460.03380.27820.09960.45720.0115-0.0491-0.06190.0718-0.01260.0870.1307-0.12730.00420.1191-0.04570.01930.12670.00810.13278.0306-32.6788-73.5766
20.22360.0360.03090.2132-0.08880.5605-0.0008-0.03690.05240.0676-0.00620.041-0.076-0.07180.00260.1120.00630.01590.1103-0.01550.125423.3347-4.8109-61.7648
30.2297-0.0328-0.03440.344-0.12540.5409-0.00580.0674-0.0559-0.10960.01850.0059-0.0015-0.0323-0.01010.1449-0.0102-0.00540.1293-0.02320.1263-4.6916-69.1128-31.142
40.2695-0.00450.06360.25830.09090.50810.00030.05150.0511-0.05490.01990.0447-0.2367-0.0909-0.01390.21850.0514-0.00180.12270.02170.1118-22.0834-41.5376-22.4937
50.33790.09890.02270.3630.03320.3866-0.00810.0161-0.0562-0.03950.0347-0.1063-0.03040.1396-0.01950.0758-0.01780.01560.1395-0.02070.137531.1912-69.0157-4.7569
60.27820.08380.08130.27570.12210.54030.0136-0.0316-0.0610.0710.0017-0.06660.14550.0916-0.01380.12880.0248-0.02120.11390.01470.129751.7601-32.4536-65.4657
70.3845-0.03870.05340.202-0.10030.46560.0036-0.00940.05910.0138-0.0112-0.0813-0.06420.14-0.01180.0764-0.0232-0.00930.1305-0.00220.139363.6068-4.9112-80.8393
80.2862-0.0670.02890.164-0.0060.49310.00350.03230.0474-0.0790.0207-0.0782-0.24180.1349-0.02060.2404-0.08550.04520.1404-0.00850.137922.3915-41.2074-21.9546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:405 OR RESID 501:504 OR RESID 601:973 ) )A3 - 405
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:405 OR RESID 501:504 OR RESID 601:973 ) )A501 - 504
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:405 OR RESID 501:504 OR RESID 601:973 ) )A601 - 973
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 3:405 OR RESID 501:503 OR RESID 601:965 ) ) OR ( CHAIN G AND RESID 601:603 ) OR ( CHAIN F AND RESID 601:603 )B3 - 405
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 3:405 OR RESID 501:503 OR RESID 601:965 ) ) OR ( CHAIN G AND RESID 601:603 ) OR ( CHAIN F AND RESID 601:603 )B501 - 503
6X-RAY DIFFRACTION2( CHAIN B AND ( RESID 3:405 OR RESID 501:503 OR RESID 601:965 ) ) OR ( CHAIN G AND RESID 601:603 ) OR ( CHAIN F AND RESID 601:603 )B601 - 965
7X-RAY DIFFRACTION2( CHAIN B AND ( RESID 3:405 OR RESID 501:503 OR RESID 601:965 ) ) OR ( CHAIN G AND RESID 601:603 ) OR ( CHAIN F AND RESID 601:603 )G601 - 603
8X-RAY DIFFRACTION2( CHAIN B AND ( RESID 3:405 OR RESID 501:503 OR RESID 601:965 ) ) OR ( CHAIN G AND RESID 601:603 ) OR ( CHAIN F AND RESID 601:603 )F601 - 603
9X-RAY DIFFRACTION3( CHAIN C AND ( RESID 2:405 OR RESID 501:504 OR RESID 601:987 ) ) OR ( CHAIN D AND RESID 601:601 )C2 - 405
10X-RAY DIFFRACTION3( CHAIN C AND ( RESID 2:405 OR RESID 501:504 OR RESID 601:987 ) ) OR ( CHAIN D AND RESID 601:601 )C501 - 504
11X-RAY DIFFRACTION3( CHAIN C AND ( RESID 2:405 OR RESID 501:504 OR RESID 601:987 ) ) OR ( CHAIN D AND RESID 601:601 )C601 - 987
12X-RAY DIFFRACTION3( CHAIN C AND ( RESID 2:405 OR RESID 501:504 OR RESID 601:987 ) ) OR ( CHAIN D AND RESID 601:601 )D601
13X-RAY DIFFRACTION4( CHAIN H AND RESID 601:601 ) OR ( CHAIN C AND RESID 988:988 ) OR ( CHAIN D AND ( RESID 2:405 OR RESID 501:504 OR RESID 602:961 ) )H601
14X-RAY DIFFRACTION4( CHAIN H AND RESID 601:601 ) OR ( CHAIN C AND RESID 988:988 ) OR ( CHAIN D AND ( RESID 2:405 OR RESID 501:504 OR RESID 602:961 ) )C988
15X-RAY DIFFRACTION4( CHAIN H AND RESID 601:601 ) OR ( CHAIN C AND RESID 988:988 ) OR ( CHAIN D AND ( RESID 2:405 OR RESID 501:504 OR RESID 602:961 ) )D2 - 405
16X-RAY DIFFRACTION4( CHAIN H AND RESID 601:601 ) OR ( CHAIN C AND RESID 988:988 ) OR ( CHAIN D AND ( RESID 2:405 OR RESID 501:504 OR RESID 602:961 ) )D501 - 504
17X-RAY DIFFRACTION4( CHAIN H AND RESID 601:601 ) OR ( CHAIN C AND RESID 988:988 ) OR ( CHAIN D AND ( RESID 2:405 OR RESID 501:504 OR RESID 602:961 ) )D602 - 961
18X-RAY DIFFRACTION5( CHAIN H AND RESID 602:604 ) OR ( CHAIN C AND RESID 989:989 ) OR ( CHAIN E AND ( RESID 2:405 OR RESID 501:503 OR RESID 601:981 ) )H602 - 604
19X-RAY DIFFRACTION5( CHAIN H AND RESID 602:604 ) OR ( CHAIN C AND RESID 989:989 ) OR ( CHAIN E AND ( RESID 2:405 OR RESID 501:503 OR RESID 601:981 ) )C989
20X-RAY DIFFRACTION5( CHAIN H AND RESID 602:604 ) OR ( CHAIN C AND RESID 989:989 ) OR ( CHAIN E AND ( RESID 2:405 OR RESID 501:503 OR RESID 601:981 ) )E2 - 405
21X-RAY DIFFRACTION5( CHAIN H AND RESID 602:604 ) OR ( CHAIN C AND RESID 989:989 ) OR ( CHAIN E AND ( RESID 2:405 OR RESID 501:503 OR RESID 601:981 ) )E501 - 503
22X-RAY DIFFRACTION5( CHAIN H AND RESID 602:604 ) OR ( CHAIN C AND RESID 989:989 ) OR ( CHAIN E AND ( RESID 2:405 OR RESID 501:503 OR RESID 601:981 ) )E601 - 981
23X-RAY DIFFRACTION6( CHAIN A AND RESID 974:974 ) OR ( CHAIN G AND RESID 604:607 ) OR ( CHAIN F AND ( RESID 2:405 OR RESID 501:503 OR RESID 604:983 ) )A974
24X-RAY DIFFRACTION6( CHAIN A AND RESID 974:974 ) OR ( CHAIN G AND RESID 604:607 ) OR ( CHAIN F AND ( RESID 2:405 OR RESID 501:503 OR RESID 604:983 ) )G604 - 607
25X-RAY DIFFRACTION6( CHAIN A AND RESID 974:974 ) OR ( CHAIN G AND RESID 604:607 ) OR ( CHAIN F AND ( RESID 2:405 OR RESID 501:503 OR RESID 604:983 ) )F2 - 405
26X-RAY DIFFRACTION6( CHAIN A AND RESID 974:974 ) OR ( CHAIN G AND RESID 604:607 ) OR ( CHAIN F AND ( RESID 2:405 OR RESID 501:503 OR RESID 604:983 ) )F501 - 503
27X-RAY DIFFRACTION6( CHAIN A AND RESID 974:974 ) OR ( CHAIN G AND RESID 604:607 ) OR ( CHAIN F AND ( RESID 2:405 OR RESID 501:503 OR RESID 604:983 ) )F604 - 983
28X-RAY DIFFRACTION7( CHAIN B AND RESID 966:969 ) OR ( CHAIN G AND ( RESID 2:405 OR RESID 501:502 OR RESID 608:956 ) ) OR ( CHAIN F AND RESID 984:986 )B966 - 969
29X-RAY DIFFRACTION7( CHAIN B AND RESID 966:969 ) OR ( CHAIN G AND ( RESID 2:405 OR RESID 501:502 OR RESID 608:956 ) ) OR ( CHAIN F AND RESID 984:986 )G2 - 405
30X-RAY DIFFRACTION7( CHAIN B AND RESID 966:969 ) OR ( CHAIN G AND ( RESID 2:405 OR RESID 501:502 OR RESID 608:956 ) ) OR ( CHAIN F AND RESID 984:986 )G501 - 502
31X-RAY DIFFRACTION7( CHAIN B AND RESID 966:969 ) OR ( CHAIN G AND ( RESID 2:405 OR RESID 501:502 OR RESID 608:956 ) ) OR ( CHAIN F AND RESID 984:986 )G608 - 956
32X-RAY DIFFRACTION7( CHAIN B AND RESID 966:969 ) OR ( CHAIN G AND ( RESID 2:405 OR RESID 501:502 OR RESID 608:956 ) ) OR ( CHAIN F AND RESID 984:986 )F984 - 986
33X-RAY DIFFRACTION8( CHAIN H AND ( RESID 3:405 OR RESID 501:502 OR RESID 605:936 ) ) OR ( CHAIN D AND RESID 962:962 )H3 - 405
34X-RAY DIFFRACTION8( CHAIN H AND ( RESID 3:405 OR RESID 501:502 OR RESID 605:936 ) ) OR ( CHAIN D AND RESID 962:962 )H501 - 502
35X-RAY DIFFRACTION8( CHAIN H AND ( RESID 3:405 OR RESID 501:502 OR RESID 605:936 ) ) OR ( CHAIN D AND RESID 962:962 )H605 - 936
36X-RAY DIFFRACTION8( CHAIN H AND ( RESID 3:405 OR RESID 501:502 OR RESID 605:936 ) ) OR ( CHAIN D AND RESID 962:962 )D962

+
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