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- PDB-6ape: Crystal Structure of Bifunctional protein FolD from Helicobacter ... -

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Basic information

Entry
Database: PDB / ID: 6ape
TitleCrystal Structure of Bifunctional protein FolD from Helicobacter pylori
ComponentsBifunctional protein FolD
KeywordsOxidoreductase / hydrolase / Seattle Structural Genomics Center for Infectious Disease / SSGCID / FolD
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / L-histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion
Similarity search - Function
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain ...Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional protein FolD
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Bifunctional protein FolD from Helicobacter pylori
Authors: SSGCID / Delker, S.L. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Other / Category: pdbx_SG_project
Revision 1.2Oct 4, 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
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_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_symmetry / _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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9956
Polymers32,6721
Non-polymers3225
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-16 kcal/mol
Surface area13850 Å2
2
A: Bifunctional protein FolD
hetero molecules

A: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,98912
Polymers65,3452
Non-polymers64510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4950 Å2
ΔGint-46 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.880, 109.040, 83.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

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Components

#1: Protein Bifunctional protein FolD


Mass: 32672.408 Da / Num. of mol.: 1 / Fragment: HepyC.00934.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: folD, HPG27_536 / Plasmid: HepyC.00934.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B5Z6U8, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Tray 291037 Morpheus A3: 10% w/v PEG 4000, 20% v/v glycerol 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride) 0.1 M MES/imidazole pH 6.5 : cryo: direct: HepyC. ...Details: Tray 291037 Morpheus A3: 10% w/v PEG 4000, 20% v/v glycerol 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride) 0.1 M MES/imidazole pH 6.5 : cryo: direct: HepyC.00934.a.B1 PS38251 at 20 mg/ml, puck mxk4-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→33.222 Å / Num. obs: 56895 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.194 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.037 / Χ2: 1.02 / Net I/σ(I): 28.34 / Num. measured all: 409285 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.497.1780.4214.1941330.9350.454100
1.49-1.537.170.3075.8540590.9630.33199.9
1.53-1.577.1950.2427.2939520.9760.261100
1.57-1.627.1980.1979.138590.9830.213100
1.62-1.677.2280.15511.6336990.9890.16899.8
1.67-1.737.240.12813.8936200.9920.13899.9
1.73-1.87.2410.10217.3634960.9950.1199.8
1.8-1.877.2460.08221.4233220.9960.08999.9
1.87-1.967.2560.06227.5632470.9980.067100
1.96-2.057.2740.05133.430690.9980.05599.9
2.05-2.167.2540.04240.2229620.9990.045100
2.16-2.297.2390.03744.8127520.9990.04100
2.29-2.457.2490.03448.2526300.9990.037100
2.45-2.657.210.03251.824560.9990.035100
2.65-2.97.2070.02855.4222630.9990.03100
2.9-3.247.1790.02660.6720600.9990.028100
3.24-3.747.1170.02463.6318220.9990.026100
3.74-4.597.0330.02366.1415620.9990.025100
4.59-6.486.9490.02365.512320.9990.025100
6.48-33.2226.1330.02561.727000.9990.02897

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12rc2_2821refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p2o

3p2o


Resolution: 1.45→33.222 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.09
RfactorNum. reflection% reflection
Rfree0.1824 1962 3.45 %
Rwork0.1669 --
obs0.1675 56863 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.53 Å2 / Biso mean: 25.3501 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 1.45→33.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 26 340 2501
Biso mean--50.1 37.08 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062318
X-RAY DIFFRACTIONf_angle_d0.7943171
X-RAY DIFFRACTIONf_chiral_restr0.075396
X-RAY DIFFRACTIONf_plane_restr0.005398
X-RAY DIFFRACTIONf_dihedral_angle_d14.968908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4501-1.48630.24071380.220638573995
1.4863-1.52650.23691500.20138664016
1.5265-1.57140.20941420.194538774019
1.5714-1.62220.23751390.181739004039
1.6222-1.68010.16061360.172338934029
1.6801-1.74740.18381350.177838854020
1.7474-1.82690.2251330.179138854018
1.8269-1.92320.1711230.181839244047
1.9232-2.04370.2031520.175538974049
2.0437-2.20150.17511430.164939284071
2.2015-2.4230.1561430.164439284071
2.423-2.77340.2031300.173939634093
2.7734-3.49360.15781300.164240034133
3.4936-33.2310.181680.148440954263
Refinement TLS params.Method: refined / Origin x: -15.045 Å / Origin y: 26.0503 Å / Origin z: -15.263 Å
111213212223313233
T0.1099 Å2-0.0091 Å20.0034 Å2-0.1353 Å2-0.0115 Å2--0.1092 Å2
L0.7409 °2-0.096 °20.044 °2-1.7834 °2-0.1704 °2--0.5305 °2
S0.0354 Å °-0.0656 Å °0.0261 Å °0.119 Å °-0.0213 Å °0.1509 Å °-0.0085 Å °-0.0966 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 288
2X-RAY DIFFRACTION1allS1 - 325
3X-RAY DIFFRACTION1allD1 - 2
4X-RAY DIFFRACTION1allB1 - 3

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