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

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Basic information

Entry
Database: PDB / ID: 3upy
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
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / Oxidoreductase, putative
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 13, 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 / 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_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.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

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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)95,5615
Polymers95,3292
Non-polymers2323
Water11,800655
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-50 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.391, 63.379, 79.334
Angle α, β, γ (deg.)68.790, 75.540, 72.070
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Oxidoreductase


Mass: 47664.562 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-FOM / 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / FOSMIDOMYCIN


Mass: 183.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10NO5P / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14-20% PEG4000, 0.1M HEPES, 0.2M magnesium chloride, 0.5 mM fosmidomycin , 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: 1.8→40 Å / Num. all: 78348 / Num. obs: 73258 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.73 / Num. unique all: 6096 / % possible all: 77.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3UPL

3upl


Resolution: 1.8→39.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.697 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 3657 5 %RANDOM
Rwork0.1627 ---
all0.1648 73258 --
obs0.1648 69601 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.56 Å2 / Biso mean: 18.47 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0.23 Å2-0.37 Å2
2---0.32 Å20.57 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 13 655 7170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226686
X-RAY DIFFRACTIONr_bond_other_d0.0010.024490
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.9849093
X-RAY DIFFRACTIONr_angle_other_deg1.068311049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9724.389262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4821546
X-RAY DIFFRACTIONr_chiral_restr0.1160.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021219
X-RAY DIFFRACTIONr_mcbond_it1.0021.54370
X-RAY DIFFRACTIONr_mcbond_other0.3361.51789
X-RAY DIFFRACTIONr_mcangle_it1.68827040
X-RAY DIFFRACTIONr_scbond_it2.96432316
X-RAY DIFFRACTIONr_scangle_it4.8024.52042
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 202 -
Rwork0.295 4081 -
all-4283 -
obs-4081 74.02 %
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)
10.5669-0.308-0.31881.24290.41411.47780.001-0.07750.00470.0626-0.01440.05730.0304-0.01410.01340.0114-0.0159-0.01590.08150.00550.062-2.7708-3.229913.5925
20.4192-0.3151-0.53711.5836-0.24691.91250.0251-0.10670.0340.1059-0.0676-0.1282-0.11380.27360.04250.0618-0.05330.00720.07160.00650.05274.8624-8.956713.3848
31.55610.10290.63032.313-1.36894.18960.0294-0.1146-0.13920.0475-0.08840.09150.22230.0790.05890.097-0.0260.0080.03830.03070.06383.1059-25.692925.2269
40.86880.43820.63811.00350.35121.31910.00950.05510.0074-0.0757-0.03450.0445-0.0119-0.00160.0250.03680.02160.02390.0461-0.00610.0477-3.15323.5643-13.7066
50.5130.4390.33821.099-0.2551.8221-0.03020.0792-0.0543-0.0745-0.0357-0.0960.06390.21150.06590.05470.0161-0.0140.03840.0060.05125.15128.8947-13.9061
61.00160.0091-0.53792.1215-0.52383.8668-0.03290.11880.1754-0.0266-0.00860.1254-0.3401-0.00620.04160.1264-0.0098-0.04190.02140.02660.07473.549925.7804-25.4434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 169
2X-RAY DIFFRACTION1A241 - 324
3X-RAY DIFFRACTION2A170 - 240
4X-RAY DIFFRACTION2A325 - 349
5X-RAY DIFFRACTION3A350 - 437
6X-RAY DIFFRACTION4B2 - 169
7X-RAY DIFFRACTION4B241 - 324
8X-RAY DIFFRACTION5B170 - 240
9X-RAY DIFFRACTION5B325 - 349
10X-RAY DIFFRACTION6B350 - 437

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