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- PDB-4zqg: Crystal structure of the Moraxella catarrhalis DOX-P Reductoisome... -

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Basic information

Entry
Database: PDB / ID: 4zqg
TitleCrystal structure of the Moraxella catarrhalis DOX-P Reductoisomerase in complex with NADH, fosmidomycin and magnesium
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / Fosmidomycin / NADH / MEP pathway / reductoisomerase
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / NADPH binding / isomerase activity / metal ion binding
Similarity search - Function
1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A ...1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBirkinshaw, R.W. / Brady, R.L.
CitationJournal: To Be Published
Title: Crystal structures of the Moraxella catarrhalis DOX-P Reductoisomerase
Authors: Birkinshaw, R.W. / Brady, R.L.
History
DepositionMay 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,32712
Polymers88,9872
Non-polymers2,34010
Water2,504139
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-59 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.719, 65.719, 390.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 5 - 412 / Label seq-ID: 6 - 413

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 1-deoxy-D-xylulose 5-phosphate reductoisomerase / DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4- ...DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4-phosphate synthase


Mass: 44493.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Gene: dxr, DR90_1378 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A076U3E6, UniProt: D5VAW2*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

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Non-polymers , 6 types, 149 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FOM / 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / FOSMIDOMYCIN


Mass: 183.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10NO5P / Comment: antibiotic*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M CHES pH 9.5, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9687 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.5→43.5 Å / Num. obs: 32902 / % possible obs: 100 % / Redundancy: 16.5 % / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.5→43.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.709 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23019 1663 5.1 %RANDOM
Rwork0.18836 ---
obs0.19046 31110 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.553 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 150 139 6333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196373
X-RAY DIFFRACTIONr_bond_other_d0.0020.026201
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9918654
X-RAY DIFFRACTIONr_angle_other_deg0.895314258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84325.242227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.941151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7341521
X-RAY DIFFRACTIONr_chiral_restr0.0850.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027144
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021333
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4213.3393299
X-RAY DIFFRACTIONr_mcbond_other2.4143.3383298
X-RAY DIFFRACTIONr_mcangle_it3.7285.0034133
X-RAY DIFFRACTIONr_mcangle_other3.7285.0054134
X-RAY DIFFRACTIONr_scbond_it3.0093.6893074
X-RAY DIFFRACTIONr_scbond_other3.0083.6913075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6385.4054521
X-RAY DIFFRACTIONr_long_range_B_refined7.23727.2347150
X-RAY DIFFRACTIONr_long_range_B_other7.22327.1117127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25718 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 106 -
Rwork0.267 2314 -
obs--99.83 %
Refinement TLS params.

L11: 0.2787 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL12 (°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)
1-0.2446-0.00730.8815-0.0761.37720.02440.0146-0.0470.0917-0.085-0.07180.17710.08930.06070.57730.0399-0.01480.44810.00970.22675.0434-15.159-16.7531
2-0.1746-0.03380.2983-0.23570.53230.00050.1275-0.01230.1087-0.0565-0.0153-0.1088-0.12270.0560.34830.1097-0.01380.3202-0.00580.0075-10.551311.8893-48.1433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 901
2X-RAY DIFFRACTION2B5 - 901

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