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- PDB-5nhs: The crystal structure of Xanthomonas albilineans N5, N10-methylen... -

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Entry
Database: PDB / ID: 5nhs
TitleThe crystal structure of Xanthomonas albilineans N5, N10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD)
ComponentsBifunctional protein FolD
KeywordsOXIDOREDUCTASE / bifunctional protein dehydrogenase cyclohydrolase
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 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Bifunctional protein FolD
Similarity search - Component
Biological speciesXanthomonas albilineans GPE PC73 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsBueno, R.V. / Guido, R.V.C. / Maluf, F.V. / Lima, G.M.A. / Oliveira, A.A.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation2013/04737-8 Brazil
Sao Paulo Research Foundation2016/16038-5 Brazil
Sao Paulo Research Foundation11/08042-9 Brazil
CitationJournal: To Be Published
Title: The crystal structure of Xanthomonas albilineans N5, N10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD)
Authors: Bueno, R.V. / Guido, R.V.C. / Maluf, F.V. / Lima, G.M.A. / Oliveira, A.A.
History
DepositionMar 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein FolD
B: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9763
Polymers62,9142
Non-polymers621
Water5,260292
1
A: Bifunctional protein FolD


Theoretical massNumber of molelcules
Total (without water)31,4571
Polymers31,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5192
Polymers31,4571
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.295, 76.404, 66.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 10 - 294 / Label seq-ID: 10 - 294

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bifunctional protein FolD


Mass: 31457.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Centro de Tecnologia Canavieira
Source: (gene. exp.) Xanthomonas albilineans GPE PC73 (bacteria)
Gene: folD, XALc_1581 / Plasmid: pETTrx / Details (production host): Thioredoxin-6HIS fusion / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D2UAL4, methenyltetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase (NADP+)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 % / Description: small crystal, thin plate, orthorhombic
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.15 M malic acid, 20% PEG 3350, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45864 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2014
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45864 Å / Relative weight: 1
ReflectionResolution: 2.11→66.64 Å / Num. obs: 36804 / % possible obs: 99.2 % / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 1.45
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 4 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.5 / Num. measured obs: 11295 / Num. unique all: 2845 / CC1/2: 0.47 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B0A

1b0a


Resolution: 2.11→66.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.541 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24054 1812 4.9 %RANDOM
Rwork0.19116 ---
obs0.19358 35007 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.668 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--1.42 Å20 Å2
3----1.37 Å2
Refinement stepCycle: 1 / Resolution: 2.11→66.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 4 292 4445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194222
X-RAY DIFFRACTIONr_bond_other_d0.0020.024152
X-RAY DIFFRACTIONr_angle_refined_deg2.1481.9865753
X-RAY DIFFRACTIONr_angle_other_deg1.14839548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79822.727165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7591545
X-RAY DIFFRACTIONr_chiral_restr0.1270.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214732
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02805
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_it1.9162.2822240
X-RAY DIFFRACTIONr_mcbond_other1.9162.2812239
X-RAY DIFFRACTIONr_mcangle_it3.0513.4052793
X-RAY DIFFRACTIONr_mcangle_other3.0513.4072794
X-RAY DIFFRACTIONr_scbond_it2.5512.6581982
X-RAY DIFFRACTIONr_scbond_other2.552.6591983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.073.8492961
X-RAY DIFFRACTIONr_long_range_B_refined7.02129.6414656
X-RAY DIFFRACTIONr_long_range_B_other7.01329.3834625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16584 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.108→2.163 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 125 -
Rwork0.295 2443 -
obs--93.83 %
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)
10.35310.47570.62371.27771.76132.6498-0.0780.07350.1505-0.04510.05180.0885-0.02370.04950.02620.0323-0.0346-0.03820.05340.050.321110.69420.132-85.184
22.2239-0.7126-2.10660.3560.49082.95510.088-0.1215-0.025-0.0691-0.05910.0075-0.06770.2384-0.02890.02470.015-0.02540.11930.03960.264722.63-2.536-76.943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 296
2X-RAY DIFFRACTION2B10 - 295

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