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- PDB-3upl: Crystal structure of the Brucella abortus enzyme catalyzing the f... -

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Basic information

Entry
Database: PDB / ID: 3upl
TitleCrystal structure of the Brucella abortus enzyme catalyzing the first committed step of the methylerythritol 4-phosphate pathway.
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / NADPH binding
Function / homology
Function and homology information


NADP binding / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Oxidoreductase DRL, catalytic domain / Aspartate/homoserine dehydrogenase, NAD-binding / SAF domain / Homoserine dehydrogenase, NAD binding domain / SAF / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Oxidoreductase, putative
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsCalisto, B.M. / Perez-Gil, J. / Fita, I. / Rodriguez-Concepcion, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of Brucella abortus deoxyxylulose-5-phosphate reductoisomerase-like (DRL) enzyme involved in isoprenoid biosynthesis.
Authors: Perez-Gil, J. / Calisto, B.M. / Behrendt, C. / Kurz, T. / Fita, I. / Rodriguez-Concepcion, M.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9107
Polymers95,5852
Non-polymers3255
Water15,349852
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-47 kcal/mol
Surface area32520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.365, 63.380, 79.123
Angle α, β, γ (deg.)68.630, 75.800, 72.700
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Oxidoreductase /


Mass: 47792.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus 2308 (bacteria)
Strain: 2308 / Gene: BAB2_0264, DRL / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YIM3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 852 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14-20% PEG4000, 0.1M HEPES, 0.2M magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 134090 / Num. obs: 129797 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 28.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.7 / Num. unique all: 12350 / % possible all: 92.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
DMMultiphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.361 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1763 6476 5 %RANDOM
Rwork0.15 ---
all0.1514 129797 --
obs0.1514 123302 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.47 Å2 / Biso mean: 13.276 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0.17 Å2-0.28 Å2
2--0.06 Å20.31 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 20 852 7388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226903
X-RAY DIFFRACTIONr_bond_other_d0.0020.024675
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9839416
X-RAY DIFFRACTIONr_angle_other_deg1.077311516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09124.224277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.193151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1831552
X-RAY DIFFRACTIONr_chiral_restr0.1230.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217821
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021277
X-RAY DIFFRACTIONr_mcbond_it1.0831.54483
X-RAY DIFFRACTIONr_mcbond_other0.3561.51828
X-RAY DIFFRACTIONr_mcangle_it1.7927255
X-RAY DIFFRACTIONr_scbond_it2.99732420
X-RAY DIFFRACTIONr_scangle_it4.9414.52133
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 422 -
Rwork0.218 8213 -
all-8635 -
obs-8213 86.48 %
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)
10.3857-0.2375-0.2290.71960.23061.01710.017-0.03290.0171-0.0141-0.00420.0061-0.0215-0.0284-0.01290.0017-0.0093-0.01560.05650.00390.0357-2.79-3.06113.021
20.1104-0.2764-0.32451.0515-0.1491.52630.02280.0132-0.0087-0.0625-0.0140.0341-0.01680.0335-0.00880.0115-0.0154-0.00360.0235-0.00120.0051.54-9.8498.569
31.21190.33180.84571.9478-0.21953.14160.0128-0.0964-0.1233-0.01510.03150.12910.2449-0.0889-0.04430.041-0.01410.00280.01290.0180.02633.218-25.77825.234
45.31710.5072-0.68367.40550.92292.22050.0375-0.08540.3607-0.08150.0466-0.2985-0.09850.2033-0.08410.0034-0.01520.00580.08630.00870.04116.435-6.76428.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 169
2X-RAY DIFFRACTION1A241 - 324
3X-RAY DIFFRACTION2A170 - 199
4X-RAY DIFFRACTION2A220 - 240
5X-RAY DIFFRACTION2A325 - 349
6X-RAY DIFFRACTION3A350 - 438
7X-RAY DIFFRACTION4A200 - 219

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