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- PDB-3ldv: 1.77 Angstrom resolution crystal structure of orotidine 5'-phosph... -

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Basic information

Entry
Database: PDB / ID: 3ldv
Title1.77 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / Orotidine 5'-Phosphate Decarboxylase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Decarboxylase / Pyrimidine biosynthesis / CSGID
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol
Similarity search - Function
: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel ...: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsHalavaty, A.S. / Shuvalova, L. / Minasov, G. / Dubrovska, I. / Winsor, J. / Glass, E.M. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.77 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Halavaty, A.S. / Shuvalova, L. / Minasov, G. / Dubrovska, I. / Winsor, J. / Glass, E.M. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7207
Polymers55,5542
Non-polymers1665
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-61 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.300, 94.675, 99.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Orotidine 5'-phosphate decarboxylase / / OMP decarboxylase / OMPDCase / OMPdecase


Mass: 27776.820 Da / Num. of mol.: 2 / Fragment: orotidine 5'-phosphate decarboxylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: pyrF, VC_1911 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPLus
References: UniProt: Q9KQT7, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 295 K / pH: 7
Details: 7mg/mL protein, The PACT Suite condition #34 (C10), 1:1 v/v ratio, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 21, 2009 / Details: BE LENSES/DIAMOND LAUE MONO
RadiationMonochromator: DIAMOND[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. obs: 43787 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.15
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.77 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L2U

1l2u


Resolution: 1.77→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.901 / SU ML: 0.07 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2205 5 %RANDOM
Rwork0.154 ---
obs0.155 41524 99.4 %-
all-41524 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.095 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å2-0 Å2-0 Å2
2---0.43 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 5 603 4245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223718
X-RAY DIFFRACTIONr_bond_other_d0.0010.022534
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.985065
X-RAY DIFFRACTIONr_angle_other_deg0.85836232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5295496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7824.211152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.31615661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.691526
X-RAY DIFFRACTIONr_chiral_restr0.0840.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
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_it0.7191.52395
X-RAY DIFFRACTIONr_mcbond_other0.2231.5962
X-RAY DIFFRACTIONr_mcangle_it1.27323886
X-RAY DIFFRACTIONr_scbond_it2.1231323
X-RAY DIFFRACTIONr_scangle_it3.6124.51179
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 164 -
Rwork0.229 2912 -
obs--95.83 %
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)
11.4040.04910.59872.4001-1.37082.8106-0.00960.09810.1385-0.0958-0.1108-0.1445-0.05930.20170.12040.0336-0.00350.02250.06230.00840.102727.92367.513516.2993
20.89150.04790.11411.4618-0.8472.13280.0099-0.0770.0411-0.01890.02680.05590.0062-0.185-0.03670.00070.00010.00290.0582-0.01710.055514.759561.959726.824
31.27590.4850.720.59760.42394.0491-0.01110.0199-0.0454-0.13580.05250.01070.1675-0.0353-0.04140.059-0.0044-0.01410.0655-0.00090.10339.296356.070411.174
47.5751-0.84690.40962.7906-2.0495.3653-0.08880.93980.1362-0.60970.0421-0.3150.50590.46310.04670.1856-0.04670.03130.223-0.03230.086425.347863.93182.6745
51.7929-0.18581.38022.0705-1.14793.8159-0.0423-0.13330.09180.2-0.0889-0.1787-0.24580.14720.13120.049-0.0369-0.02680.0965-0.02410.094130.890862.889945.0979
60.86910.14910.12161.3648-0.54311.6634-0.0005-0.0386-0.0359-0.0976-0.0326-0.12850.14090.08090.03310.01610.0020.01710.0490.00120.072927.175150.665933.1525
71.16730.308-0.34582.77060.01492.972-0.0176-0.1720.00080.2095-0.02890.00360.1565-0.01380.04640.0536-0.0013-0.00330.05880.00390.076921.276642.542145.713
81.06680.59140.49463.70760.24741.2850.0762-0.23370.06560.4487-0.1231-0.0428-0.02-0.05180.04690.1075-0.0515-0.01240.1307-0.0210.074427.525754.840756.0221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 50
2X-RAY DIFFRACTION2A51 - 134
3X-RAY DIFFRACTION3A135 - 207
4X-RAY DIFFRACTION4A208 - 230
5X-RAY DIFFRACTION5B2 - 43
6X-RAY DIFFRACTION6B44 - 140
7X-RAY DIFFRACTION7B141 - 194
8X-RAY DIFFRACTION8B195 - 231

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