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- PDB-1z9w: Tetrameric structure of apo-7,8-Dihydroneopterin Aldolase from My... -

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Basic information

Entry
Database: PDB / ID: 1z9w
TitleTetrameric structure of apo-7,8-Dihydroneopterin Aldolase from Mycobacterium tuberculosis
ComponentsDihydroneopterin aldolase
KeywordsLYASE / FOLB / MYCOBACTERIUM TUBERCULOSIS / Structural Genomics / TB Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / PSI / Protein Structure Initiative
Function / homology
Function and homology information


7,8-dihydroneopterin oxygenase / 7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / encapsulin nanocompartment / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / isomerase activity / oxidoreductase activity / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydroneopterin aldolase / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGoulding, C.W. / Apostol, M.I. / Sawaya, M.R. / Philips, M. / Parseghian, A. / Eisenberg, D. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme.
Authors: Goulding, C.W. / Apostol, M.I. / Sawaya, M.R. / Phillips, M. / Parseghian, A. / Eisenberg, D.
History
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionApr 19, 2005ID: 1R7K
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: 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
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: Dihydroneopterin aldolase


Theoretical massNumber of molelcules
Total (without water)14,5741
Polymers14,5741
Non-polymers00
Water45025
1
A: Dihydroneopterin aldolase

A: Dihydroneopterin aldolase

A: Dihydroneopterin aldolase

A: Dihydroneopterin aldolase


Theoretical massNumber of molelcules
Total (without water)58,2984
Polymers58,2984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area6870 Å2
ΔGint-34 kcal/mol
Surface area20840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.957, 72.957, 42.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Dihydroneopterin aldolase / DHNA


Mass: 14574.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Gene: folB / Plasmid: PET22B+-RV3607C / Production host: Escherichia coli (E. coli)
References: UniProt: P0A580, UniProt: P9WNC5*PLUS, dihydroneopterin aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 4000, SODIUM ACETATE, PH 4.6, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9786 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 8, 2003
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 3990 / % possible obs: 99 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 31.3
Reflection shellResolution: 2.5→3 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 7.6 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBU

1nbu


Resolution: 2.5→51.57 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.838 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.068 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23429 393 10 %RANDOM
Rwork0.17854 ---
all0.18441 3548 --
obs0.18441 3548 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.451 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 0 25 846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022835
X-RAY DIFFRACTIONr_angle_refined_deg2.2611.9421142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8645106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.58523.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67915123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.087159
X-RAY DIFFRACTIONr_chiral_restr0.1390.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02649
X-RAY DIFFRACTIONr_nbd_refined0.2410.2333
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.26
X-RAY DIFFRACTIONr_mcbond_it1.3631.5550
X-RAY DIFFRACTIONr_mcangle_it2.4752869
X-RAY DIFFRACTIONr_scbond_it3.5653313
X-RAY DIFFRACTIONr_scangle_it5.5854.5273
LS refinement shellResolution: 2.5→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 24 -
Rwork0.178 264 -
obs--96.97 %
Refinement TLS params.Method: refined / Origin x: 52.8478 Å / Origin y: 30.4407 Å / Origin z: 37.3967 Å
111213212223313233
T-0.0138 Å20.0192 Å2-0.0211 Å2--0.005 Å20.0206 Å2--0.0397 Å2
L1.2413 °20.3565 °2-0.0537 °2-3.4304 °21.1086 °2--0.9018 °2
S-0.0776 Å °0.0023 Å °-0.1646 Å °0.0322 Å °0.0584 Å °-0.4195 Å °-0.094 Å °0.0262 Å °0.0192 Å °

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