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- PDB-1twy: Crystal structure of an ABC-type phosphate transport receptor fro... -

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Basic information

Entry
Database: PDB / ID: 1twy
TitleCrystal structure of an ABC-type phosphate transport receptor from Vibrio cholerae
ComponentsABC transporter, periplasmic substrate-binding protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ABC transporter / NYSGXRC target / Protein Structure Initiative / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


phosphate ion transport / phosphate ion binding / periplasmic space / cell adhesion / extracellular region / metal ion binding
Similarity search - Function
PBP superfamily domain / Phosphate binding protein / : / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / : / Phosphate-binding protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsRamagopal, U.A. / Patskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical ABC-type phosphate transporter
Authors: Ramagopal, U.A. / Patskovsky, Y. / Almo, S.C.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_database_related ...audit_author / pdbx_database_related / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_database_related.db_name ..._audit_author.identifier_ORCID / _pdbx_database_related.db_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, periplasmic substrate-binding protein
B: ABC transporter, periplasmic substrate-binding protein
C: ABC transporter, periplasmic substrate-binding protein
D: ABC transporter, periplasmic substrate-binding protein
E: ABC transporter, periplasmic substrate-binding protein
F: ABC transporter, periplasmic substrate-binding protein
G: ABC transporter, periplasmic substrate-binding protein
H: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,29917
Polymers256,5158
Non-polymers7849
Water25,4371412
1
A: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1843
Polymers32,0641
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers32,0641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers32,0641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers32,0641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers32,0641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers32,0641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers32,0641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers32,0641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: ABC transporter, periplasmic substrate-binding protein
B: ABC transporter, periplasmic substrate-binding protein
hetero molecules

C: ABC transporter, periplasmic substrate-binding protein
D: ABC transporter, periplasmic substrate-binding protein
hetero molecules

E: ABC transporter, periplasmic substrate-binding protein
F: ABC transporter, periplasmic substrate-binding protein
hetero molecules

G: ABC transporter, periplasmic substrate-binding protein
H: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,29917
Polymers256,5158
Non-polymers7849
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_454x-1,y,z-11
Buried area16480 Å2
ΔGint-131 kcal/mol
Surface area80390 Å2
MethodPISA
10
A: ABC transporter, periplasmic substrate-binding protein
B: ABC transporter, periplasmic substrate-binding protein
hetero molecules

C: ABC transporter, periplasmic substrate-binding protein
D: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6629
Polymers128,2574
Non-polymers4045
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7540 Å2
ΔGint-66 kcal/mol
Surface area41280 Å2
MethodPISA
11
E: ABC transporter, periplasmic substrate-binding protein
F: ABC transporter, periplasmic substrate-binding protein
hetero molecules

G: ABC transporter, periplasmic substrate-binding protein
H: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6378
Polymers128,2574
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7400 Å2
ΔGint-57 kcal/mol
Surface area40650 Å2
MethodPISA
12
A: ABC transporter, periplasmic substrate-binding protein
hetero molecules

D: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3435
Polymers64,1292
Non-polymers2143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1830 Å2
ΔGint-33 kcal/mol
Surface area22900 Å2
MethodPISA
13
F: ABC transporter, periplasmic substrate-binding protein
hetero molecules

G: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3194
Polymers64,1292
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1690 Å2
ΔGint-24 kcal/mol
Surface area22110 Å2
MethodPISA
14
B: ABC transporter, periplasmic substrate-binding protein
hetero molecules

C: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3194
Polymers64,1292
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1710 Å2
ΔGint-23 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.630, 103.932, 126.687
Angle α, β, γ (deg.)90.00, 102.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ABC transporter, periplasmic substrate-binding protein


Mass: 32064.373 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Species: Vibrio cholerae / Strain: N16961 / Production host: Escherichia coli (E. coli) / References: GenBank: 15601562, UniProt: Q9KLD9*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1412 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.5
Details: PegMME 20%, Kcl 0.2M, Tris-Bis, pH 6.5, LIQUID DIFFUSION

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A11.009
SYNCHROTRONNSLS X29A20.979
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMay 20, 2004
ADSC QUANTUM 42CCDJun 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
20.9791
ReflectionResolution: 1.65→20 Å / Num. all: 256149 / Num. obs: 256149 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.82 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.081 / Net I/σ(I): 22.21
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.02 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→19.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.951 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23062 7738 3 %RANDOM
Rwork0.19275 ---
obs0.19388 248059 99.69 %-
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: 24.066 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15285 0 41 1412 16738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02215480
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213993
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.94820970
X-RAY DIFFRACTIONr_angle_other_deg1.066332690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56851963
X-RAY DIFFRACTIONr_chiral_restr0.1490.22484
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217080
X-RAY DIFFRACTIONr_gen_planes_other0.010.022895
X-RAY DIFFRACTIONr_nbd_refined0.2240.23032
X-RAY DIFFRACTIONr_nbd_other0.2550.216323
X-RAY DIFFRACTIONr_nbtor_other0.0920.29259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.21035
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.2239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.274
X-RAY DIFFRACTIONr_mcbond_it2.81839791
X-RAY DIFFRACTIONr_mcangle_it4.19515867
X-RAY DIFFRACTIONr_scbond_it5.79965689
X-RAY DIFFRACTIONr_scangle_it8.20185103
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 563
Rwork0.215 18060

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