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- PDB-4cq8: Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in com... -

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Basic information

Entry
Database: PDB / ID: 4cq8
TitlePlasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with Genz-669178
ComponentsDIHYDROOROTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DHODH
Function / homology
Function and homology information


Pyrimidine biosynthesis / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / nucleotide binding / plasma membrane
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-JBW / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.98 Å
AuthorsRowland, P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: In Vitro Resistance Selections for Plasmodium Falciparum Dihydroorotate Dehydrogenase Inhibitors Give Mutants with Multiple Point Mutations in the Drug-Binding Site and Altered Growth.
Authors: Ross, L.S. / Javier Gamo, F. / Lafuente-Monasterio, M.J.E. / Singh, O.M.P. / Rowland, P. / Wiegand, R.C. / Wirth, D.F.
History
DepositionFeb 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE
B: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6418
Polymers90,7722
Non-polymers1,8706
Water10,233568
1
A: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3214
Polymers45,3861
Non-polymers9353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3214
Polymers45,3861
Non-polymers9353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.820, 69.130, 103.850
Angle α, β, γ (deg.)90.00, 103.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DIHYDROOROTATE DEHYDROGENASE


Mass: 45385.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUES 384-413 DELETED
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q54A96, UniProt: Q08210*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-JBW / 5-(4-cyano-2-methyl-1H-benzimidazol-1-yl)-N-cyclopropylthiophene-2-carboxamide


Mass: 322.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14N4OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.84 Å3/Da / Density % sol: 56.66 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: CO-CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20 DEGREES C FROM A SOLUTION OF PROTEIN AT 10 MG/ML IN BUFFER (10 MM HEPES PH 7.8, 100 MM SODIUM CHLORIDE, 5% GLYCEROL, 10 MM DTT, 1 MM LDAO) ...Details: CO-CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20 DEGREES C FROM A SOLUTION OF PROTEIN AT 10 MG/ML IN BUFFER (10 MM HEPES PH 7.8, 100 MM SODIUM CHLORIDE, 5% GLYCEROL, 10 MM DTT, 1 MM LDAO) CONTAINING 2 MM L-DIHYDROOROTATE, 2 MM GENZ-669178, 10 MM LDAO, MIXED WITH AN EQUAL VOLUME OF PRECIPITANT (24% PEG 3350, 0.2M LITHIUM CHLORIDE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 69060 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 37.56 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / % possible all: 85.3

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.98→46.86 Å / Cor.coef. Fo:Fc: 0.9532 / Cor.coef. Fo:Fc free: 0.9513 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 2784 4.03 %RANDOM
Rwork0.17 ---
obs0.1708 69057 97.28 %-
Displacement parametersBiso mean: 52.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.4182 Å20 Å22.987 Å2
2--8.0936 Å20 Å2
3----8.5118 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: LAST / Resolution: 1.98→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 130 568 6688
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016248HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.018432HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2240SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes986HARMONIC5
X-RAY DIFFRACTIONt_it6248HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion822SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7635SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2738 186 4.3 %
Rwork0.233 4139 -
all0.2347 4325 -
obs--97.28 %
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)
11.28580.03580.13932.89330.32340.74590.01980.101-0.0906-0.2772-0.06650.2476-0.0224-0.03680.0467-0.26610.0068-0.0796-0.1936-0.00710.185511.43439.099342.3482
21.52470.46720.38913.6370.03461.26450.0775-0.09250.06690.3921-0.0655-0.0558-0.04070.1017-0.012-0.10040.0088-0.0601-0.2108-0.0309-0.069847.404-7.256511.315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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