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- PDB-2zza: Moritella profunda Dihydrofolate reductase complex with NADP+ and... -

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Basic information

Entry
Database: PDB / ID: 2zza
TitleMoritella profunda Dihydrofolate reductase complex with NADP+ and Folate
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Dihydrofolate reductase / Folic acid / NADP / deep-sea / high pressure / low temperature / Moritella profunda / piezophilic / psychrophilic / psychropiezophilic
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMoritella profunda (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHata, K. / Tanaka, T. / Murakami, C. / Ohmae, E. / Gekko, K. / Shiro, Y. / Akasaka, K.
CitationJournal: To be Published
Title: Moritella profunda Dihydrofolate reductase complex with NADP+ and Folate
Authors: Hata, K. / Tanaka, T. / Murakami, C. / Ohmae, E. / Gekko, K. / Shiro, Y. / Akasaka, K.
History
DepositionFeb 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1617
Polymers36,5532
Non-polymers2,6085
Water5,044280
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7004
Polymers18,2771
Non-polymers1,4233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4623
Polymers18,2771
Non-polymers1,1852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.598, 77.458, 159.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dihydrofolate reductase


Mass: 18276.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moritella profunda (bacteria) / Strain: 2674T / Gene: dyrA / Plasmid: pUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q70YQ6, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N7O6
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THE FIRST RESIDUE OF THE PROTEIN IS VAL.

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M sodium citrate, 15% PEG4000, 0.1 Hexammine Cobalt (III) chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 13, 2007
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 21062 / Num. obs: 21062 / % possible obs: 85.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.073 / Net I/σ(I): 2.82
Reflection shellHighest resolution: 2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.82 / Num. unique all: 21062 / Rsym value: 0.299 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDS

1dds


Resolution: 2→31.33 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.224 1045 4.3 %
Rwork0.201 19988 -
obs-21033 87 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.935 Å2
Displacement parametersBiso max: 60.12 Å2 / Biso mean: 26.807 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1-7.998 Å20 Å20 Å2
2---14.436 Å20 Å2
3---6.438 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→31.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 176 280 3010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1951.5
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_mcangle_it1.8852
X-RAY DIFFRACTIONc_scangle_it2.8222.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 151 4.5 %
Rwork0.28 3177 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3FOL3_param.txt
X-RAY DIFFRACTION4CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION5CNS_TOPPAR:ion.param
X-RAY DIFFRACTION6NAP3_param.txt
X-RAY DIFFRACTION7PEG400_param.txt

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