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- PDB-4o0k: Crystal structure of 1-pyrroline-4-hydroxy-2-carboxylate deaminas... -

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Basic information

Entry
Database: PDB / ID: 4o0k
TitleCrystal structure of 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis with covalently bound substrate
ComponentsDihydrodipicolinate synthetase
KeywordsLYASE / SSGCID / Brucella melitensis / pyruvate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Dihydrodipicolinate synthetase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis with covalently bound substrate
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Fox III, D. / Lorimer, D. / Edwards, T.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8533
Polymers35,7291
Non-polymers1242
Water7,332407
1
A: Dihydrodipicolinate synthetase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)215,11818
Polymers214,3736
Non-polymers74512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area17150 Å2
ΔGint-2 kcal/mol
Surface area63720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.280, 95.280, 125.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-792-

HOH

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Components

#1: Protein Dihydrodipicolinate synthetase


Mass: 35728.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: biotype 2 (strain ATCC 23457) / Gene: BMEA_B0240 / Plasmid: BrmeB.01563.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0RKH4, EC: 3.5.4.22
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: EmeraldBio MCSG1 screen, a11: 10% PEG 4000, 200mM MgCl2, 100mM MES/NaOH; crystals soaked over night with 20mM pyruvate; cryo 20% EG; BrmeB.01563.a.B1.PS01874 at 19.3mg/ml, tray 247709a11, ...Details: EmeraldBio MCSG1 screen, a11: 10% PEG 4000, 200mM MgCl2, 100mM MES/NaOH; crystals soaked over night with 20mM pyruvate; cryo 20% EG; BrmeB.01563.a.B1.PS01874 at 19.3mg/ml, tray 247709a11, puck amw3-4, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 3, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 54227 / Num. obs: 54188 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 23.908 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.11
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.540.5184.142837839291100
1.54-1.580.4135.072756938171100
1.58-1.630.3286.31271403752199.9
1.63-1.680.2677.49263433636199.9
1.68-1.730.2328.52553835191100
1.73-1.790.1910.012492534291100
1.79-1.860.15511.95238623279199.9
1.86-1.940.12414.212323231931100
1.94-2.020.10117.112220730571100
2.02-2.120.08519.882133029371100
2.12-2.240.07422.592039128031100
2.24-2.370.06724.691922826541100
2.37-2.540.06226.551807925051100
2.54-2.740.05928.41675723331100
2.74-30.05331.111558121801100
3-3.350.05133.361402919751100
3.35-3.870.04835.64124111753199.9
3.87-4.740.04636.64105481517199.9
4.74-6.710.04735.7581101204199.8
6.71-500.04734.354270716197

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4mpq

4mpq


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1804 / WRfactor Rwork: 0.1583 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8888 / SU B: 2.203 / SU ML: 0.042 / SU R Cruickshank DPI: 0.066 / SU Rfree: 0.0648 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2729 5 %RANDOM
Rwork0.1583 ---
obs0.1593 54187 99.92 %-
all-54227 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.81 Å2 / Biso mean: 20.0484 Å2 / Biso min: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 8 407 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192625
X-RAY DIFFRACTIONr_bond_other_d0.0010.022507
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9573579
X-RAY DIFFRACTIONr_angle_other_deg0.8722.9985769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05623.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9761517
X-RAY DIFFRACTIONr_chiral_restr0.10.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02615
X-RAY DIFFRACTIONr_mcbond_it0.9781.2221330
X-RAY DIFFRACTIONr_mcbond_other0.9651.221329
X-RAY DIFFRACTIONr_mcangle_it1.5271.8251664
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 205 -
Rwork0.199 3717 -
all-3922 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 4.584 Å / Origin y: 31.321 Å / Origin z: 12.678 Å
111213212223313233
T0.0487 Å2-0.0002 Å20.0177 Å2-0.0305 Å2-0.0126 Å2--0.0148 Å2
L0.2546 °20.0424 °2-0.0357 °2-0.5651 °2-0.3457 °2--0.4623 °2
S-0.0173 Å °0.0002 Å °-0.0258 Å °-0.0125 Å °-0.0256 Å °-0.0265 Å °0.0502 Å °0.0005 Å °0.0429 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 320
2X-RAY DIFFRACTION1A400 - 401
3X-RAY DIFFRACTION1A501 - 907

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