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- PDB-4z7f: Crystal structure of FolT bound with folic acid -

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Basic information

Entry
Database: PDB / ID: 4z7f
TitleCrystal structure of FolT bound with folic acid
ComponentsFolate ECF transporter
KeywordsTRANSPORT PROTEIN / folate transporter / gating mechanism / folate binding and release / group II ECF transporters / ATP-binding cassette transporters
Function / homology
Function and homology information


transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function
ECF transporter S component, folate family / ECF transporter, substrate-specific component / ECF transporter, substrate-specific component / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FOLIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.194 Å
AuthorsZhao, Q. / Wang, C.C. / Wang, C.Y. / Zhang, P.
CitationJournal: Nat Commun / Year: 2015
Title: Structures of FolT in substrate-bound and substrate-released conformations reveal a gating mechanism for ECF transporters
Authors: Zhao, Q. / Wang, C.C. / Wang, C.Y. / Guo, H. / Bao, Z.H. / Zhang, M.H. / Zhang, P.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Nov 8, 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Folate ECF transporter
B: Folate ECF transporter
C: Folate ECF transporter
D: Folate ECF transporter
E: Folate ECF transporter
F: Folate ECF transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,39512
Polymers134,7476
Non-polymers2,6486
Water0
1
A: Folate ECF transporter
B: Folate ECF transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7984
Polymers44,9162
Non-polymers8832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-19 kcal/mol
Surface area17860 Å2
MethodPISA
2
C: Folate ECF transporter
D: Folate ECF transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7984
Polymers44,9162
Non-polymers8832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-19 kcal/mol
Surface area17320 Å2
MethodPISA
3
E: Folate ECF transporter
F: Folate ECF transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7984
Polymers44,9162
Non-polymers8832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-14 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.752, 92.752, 183.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Folate ECF transporter / Ef-FolT / Uncharacterized protein


Mass: 22457.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: EF_0940 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q837A3
#2: Chemical
ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H19N7O6

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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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 15% (w/v) polyethylene glycol 2000, 0.5M NaCl, 0.1M sodium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.194→40 Å / Num. obs: 28978 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 72.91 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.093 / Rrim(I) all: 0.15 / Χ2: 1.68 / Net I/av σ(I): 11.375 / Net I/σ(I): 6.3 / Num. measured all: 101633
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.2-3.313.529020.820.8551.11499.3
3.31-3.453.629530.8960.5931.23999.20.976
3.45-3.63.628990.9570.3811.36499.60.6260.738
3.6-3.793.629450.9780.2781.44599.40.4560.538
3.79-4.033.629370.9640.2261.63299.50.3680.435
4.03-4.343.628630.9860.1342.01698.50.2150.255
4.34-4.783.529020.9850.1072.08197.60.1690.202
4.78-5.473.429070.9810.1022.29997.70.1610.193
5.47-6.883.428570.9870.0771.76597.60.1230.146
6.88-403.228130.9950.0361.95494.80.0560.067

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HUQ

4huq


Resolution: 3.194→33.569 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 47.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3564 2000 8.98 %1
Rwork0.2934 ---
obs0.299 22266 76.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.194→33.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7670 0 192 0 7862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178153
X-RAY DIFFRACTIONf_angle_d2.4711113
X-RAY DIFFRACTIONf_dihedral_angle_d20.5432686
X-RAY DIFFRACTIONf_chiral_restr0.1291268
X-RAY DIFFRACTIONf_plane_restr0.0151297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1945-3.27430.4877340.2864354X-RAY DIFFRACTION19
3.2743-3.36280.2798510.2831469X-RAY DIFFRACTION25
3.3628-3.46160.4289650.2898668X-RAY DIFFRACTION35
3.4616-3.57320.424860.2964877X-RAY DIFFRACTION46
3.5732-3.70080.39081300.32031318X-RAY DIFFRACTION69
3.7008-3.84880.42291800.33741857X-RAY DIFFRACTION98
3.8488-4.02360.38431880.31621881X-RAY DIFFRACTION98
4.0236-4.23540.37211790.30151820X-RAY DIFFRACTION97
4.2354-4.50020.36071850.27681859X-RAY DIFFRACTION98
4.5002-4.84670.36221860.28171817X-RAY DIFFRACTION96
4.8467-5.33270.39541680.29351840X-RAY DIFFRACTION97
5.3327-6.10030.40581800.32481875X-RAY DIFFRACTION98
6.1003-7.67060.34221810.32161863X-RAY DIFFRACTION97
7.6706-33.57120.30291870.26461768X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -7.7366 Å / Origin y: 32.4503 Å / Origin z: 20.4339 Å
111213212223313233
T0.538 Å2-0.0016 Å2-0.0493 Å2-0.6147 Å20.0097 Å2--0.6837 Å2
L0.0559 °20.055 °2-0.105 °2-0.4499 °2-0.1002 °2--1.0232 °2
S0.0089 Å °0.076 Å °-0.0041 Å °-0.0621 Å °-0.0218 Å °0.0965 Å °0.0181 Å °-0.3152 Å °0.0162 Å °
Refinement TLS groupSelection details: all

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