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- PDB-3puw: Crystal Structure of an outward-facing MBP-Maltose transporter co... -

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Basic information

Entry
Database: PDB / ID: 3puw
TitleCrystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-AlF4
Components
  • (Maltose transport system permease protein ...) x 2
  • Maltose-binding periplasmic protein
  • Maltose/maltodextrin import ATP-binding protein MalK
KeywordsHYDROLASE/TRANSPORT PROTEIN / ATP Binding Cassette Nucleotide Binding Domain Substrate Binding Protein Transmembrane Domain / ABC Transporter importer ATPase / ATP binding Maltodextrin binding / transmembrane integral membrane / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / DNA-binding transcription factor binding / periplasmic space / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain ...MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / MetI-like fold / MetI-like / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Nucleic acid-binding proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / Periplasmic binding protein-like II / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / D-Maltodextrin-Binding Protein; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Roll / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Chem-PGV / Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOldham, M.L. / Chen, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Snapshots of the maltose transporter during ATP hydrolysis.
Authors: Oldham, M.L. / Chen, J.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Maltose-binding periplasmic protein
F: Maltose transport system permease protein malF
G: Maltose transport system permease protein malG
A: Maltose/maltodextrin import ATP-binding protein MalK
B: Maltose/maltodextrin import ATP-binding protein MalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,72823
Polymers215,2905
Non-polymers9,43818
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31170 Å2
ΔGint-168 kcal/mol
Surface area76210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.881, 97.344, 112.336
Angle α, β, γ (deg.)85.76, 79.42, 72.45
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 3 molecules EAB

#1: Protein Maltose-binding periplasmic protein / MMBP / Maltodextrin-binding protein


Mass: 41622.047 Da / Num. of mol.: 1 / Fragment: unp residues 27-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4034, ECDH10B_4223, JW3994, malE / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#4: Protein Maltose/maltodextrin import ATP-binding protein MalK


Mass: 42184.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4035, ECDH10B_4224, JW3995, malK / Production host: Escherichia coli (E. coli) / References: UniProt: P68187, EC: 3.6.3.19

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Maltose transport system permease protein ... , 2 types, 2 molecules FG

#2: Protein Maltose transport system permease protein malF


Mass: 57052.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4033, ECDH10B_4222, JW3993, malF / Production host: Escherichia coli (E. coli) / References: UniProt: P02916
#3: Protein Maltose transport system permease protein malG


Mass: 32246.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4032, ECDH10B_4221, JW3992, malG / Production host: Escherichia coli (E. coli) / References: UniProt: P68183

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Sugars , 1 types, 1 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 290 molecules

#6: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#7: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 27 % PEG 400, 0.1 M HEPES, 10 mM magnesium chloride, 50 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97965 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 10, 2009
RadiationMonochromator: double crystal monochromator and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 93125 / Num. obs: 93125 / % possible obs: 60.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.459 / % possible all: 16.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.99 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.644 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 4819 5 %RANDOM
Rwork0.22022 ---
obs0.22194 91058 66.49 %-
all-93125 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.504 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0.93 Å2-1.03 Å2
2--0.51 Å20.68 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14602 0 287 273 15162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.98420752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.62751895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58424.313633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65152517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2311578
X-RAY DIFFRACTIONr_chiral_restr0.0640.22368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111321
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2221.59392
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.419215146
X-RAY DIFFRACTIONr_scbond_it0.57735895
X-RAY DIFFRACTIONr_scangle_it0.974.55599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 110 -
Rwork0.279 1813 -
obs--18.28 %
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)
14.31750.11050.45057.80832.61735.268-0.03570.0897-0.0850.1734-0.01080.80721.4732-0.85440.04650.7646-0.16620.19070.37270.10440.29758.0882.4717.38
20.9171-0.1211-0.0363.64041.57672.3224-0.0025-0.0878-0.0429-0.03010.0848-0.16850.44260.1683-0.08230.18780.08480.07060.07550.04250.119122.09686.6017.522
34.27672.5841-1.32727.2684-1.93956.06150.00680.22030.0338-1.2460.191-0.11990.52330.146-0.19780.95690.12180.10930.1224-0.09910.169621.4878.584-13.962
410.5747-2.0087-0.27.40450.07412.2027-0.1995-0.72310.91680.09090.0211-0.9041-0.43870.6120.17840.4621-0.09560.33080.27210.02420.594835.681120.165-0.683
52.3923-0.2278-0.91013.4030.26762.55990.04590.23830.1761-0.8320.034-0.1508-0.3628-0.1006-0.07990.36720.02380.1290.09060.02890.120.846109.811-2.102
64.11061.7474-0.8716.4292-2.33582.62860.19230.0228-0.3585-0.728-0.2014-1.94550.62971.13070.00910.58720.37040.39370.8199-0.21061.131949.92587.93-3.795
71.0504-0.276-0.42642.384-0.23523.56910.0303-0.0257-0.0550.2704-0.11890.175-0.3184-0.41830.08860.14150.01910.04850.1723-0.14160.1747-13.338147.49167.741
82.7709-0.4684-0.28253.88140.98744.47480.00030.26310.2095-0.1593-0.1710.5619-1.1767-1.01070.17060.74730.5984-0.07290.5069-0.06020.3529-24.114164.74546.24
90.6694-0.2668-0.13661.94820.09453.17740.17680.05140.12910.0469-0.20250.1635-0.9951-0.66770.02570.45040.24870.04110.2283-0.10010.1901-16.18158.71355.279
1015.9705-3.0606-4.43079.0674.15119.7767-1.4651-1.7537-0.53432.60140.8890.85412.25160.6610.57611.37220.1190.38450.38980.09260.1232-0.231103.97460.516
110.5824-0.5711-1.06181.56711.33443.7809-0.19870.2292-0.22380.5767-0.29930.47530.5338-0.86190.49790.317-0.19850.21030.2736-0.13830.3443-22.102130.64175.233
121.2183-1.0117-1.07311.93921.23432.44780.11430.2487-0.0284-0.4329-0.31810.11-0.3406-0.52680.20380.1850.1179-0.03110.2227-0.0680.1517-6.076135.76128.069
130.7548-0.636-0.52933.56370.49582.8280.2048-0.0740.2287-0.2485-0.0932-0.5139-0.65460.2527-0.11160.1702-0.03230.08190.1925-0.02240.359810.148142.47939.558
144.8671-2.479-1.08924.89184.35559.7641-0.05340.1959-0.43780.3448-0.54460.33320.7787-1.14980.5980.3844-0.22830.25610.2545-0.06340.4631-6.371116.96447.813
150.4383-0.5233-0.78012.3242.18932.4340.0153-0.07770.09170.07430.0314-0.13670.09710.0835-0.04680.12230.03320.01330.1732-0.01660.228.058125.02740.484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 29
2X-RAY DIFFRACTION2A30 - 319
3X-RAY DIFFRACTION2A2501
4X-RAY DIFFRACTION2A3001
5X-RAY DIFFRACTION2A1501
6X-RAY DIFFRACTION3A320 - 372
7X-RAY DIFFRACTION4B2 - 29
8X-RAY DIFFRACTION5B30 - 228
9X-RAY DIFFRACTION5B1502
10X-RAY DIFFRACTION5B2502
11X-RAY DIFFRACTION5B3002
12X-RAY DIFFRACTION6B229 - 369
13X-RAY DIFFRACTION7E1 - 123
14X-RAY DIFFRACTION8E124 - 198
15X-RAY DIFFRACTION9E199 - 374
16X-RAY DIFFRACTION9F5004
17X-RAY DIFFRACTION10F10 - 53
18X-RAY DIFFRACTION11F54 - 273
19X-RAY DIFFRACTION12F274 - 503
20X-RAY DIFFRACTION12F2000
21X-RAY DIFFRACTION12F4001
22X-RAY DIFFRACTION12F4010
23X-RAY DIFFRACTION13G9 - 112
24X-RAY DIFFRACTION14G113 - 155
25X-RAY DIFFRACTION15G156 - 296
26X-RAY DIFFRACTION15G4003 - 4009
27X-RAY DIFFRACTION15F4002 - 4008

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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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