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- PDB-3nrs: Crystal structure of ligand-free bifunctional folylpolyglutamate ... -

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Basic information

Entry
Database: PDB / ID: 3nrs
TitleCrystal structure of ligand-free bifunctional folylpolyglutamate synthase/dihydrofolate synthase from yersinia pestis c092
ComponentsDihydrofolate:folylpolyglutamate synthetase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TETRAHYDROFOLATE SYNTHASE
Function / homology
Function and homology information


dihydrofolate synthase activity / tetrahydrofolylpolyglutamate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily ...Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Dihydrofolate synthase/folylpolyglutamate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNocek, B. / Maltseva, N. / Makowska-grzyska, M. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of ligand-free bifunctional folylpolyglutamate synthase/dihydrofolate synthase from yersinia pestis c092
Authors: Nocek, B. / Maltseva, N. / Makowska-grzyska, M. / Papazisi, L. / Anderson, W. / Joachimiak, A.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Dihydrofolate:folylpolyglutamate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4728
Polymers47,5511
Non-polymers9227
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.628, 83.275, 126.740
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 Dihydrofolate:folylpolyglutamate synthetase / Putative FolC bifunctional protein


Mass: 47550.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: folC, YP_2395, y1602 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8D0U0
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES, 1.0 M Na/K Tartrate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.78→40 Å / Num. all: 64300 / Num. obs: 63699 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 30
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N2A

3n2a


Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.043 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19222 3112 5.1 %RANDOM
Rwork0.17257 ---
all0.18 61500 --
obs0.1736 58317 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.006 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---0.22 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 60 312 3423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213170
X-RAY DIFFRACTIONr_bond_other_d0.0010.022092
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9714307
X-RAY DIFFRACTIONr_angle_other_deg1.05535100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4025399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81523.796137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09315497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8211523
X-RAY DIFFRACTIONr_chiral_restr0.1310.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
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_it1.0491.51990
X-RAY DIFFRACTIONr_mcbond_other0.3191.5817
X-RAY DIFFRACTIONr_mcangle_it1.85323175
X-RAY DIFFRACTIONr_scbond_it2.82331180
X-RAY DIFFRACTIONr_scangle_it4.5754.51131
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 220 -
Rwork0.262 4246 -
obs--98.2 %
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)
10.81320.62652.14162.6330.03699.01-0.6858-0.2591-0.0456-0.42550.12250.6212-1.194-0.63960.56320.29860.1745-0.07940.00560.05350.1612-13.383834.75088.0677
2-0.06640.15060.15570.5378-0.00171.42410.0071-0.0080.0206-0.00920.0702-0.00650.0714-0.1626-0.07730.168-0.00470.01030.18380.01520.166-4.636717.191319.3403
31.1320.72610.38420.72330.76661.8538-0.00130.03920.033-0.06610.0195-0.01380.0019-0.0095-0.01820.16160.0091-0.0010.20070.02610.1484-1.467922.33967.3106
4-0.2773-1.8272-0.69652.20871.10194.7706-0.1360.0148-0.1597-0.18270.2646-0.0081-0.6545-0.3857-0.12860.2640.077-0.09780.20880.09480.1434-14.47132.09644.0192
5-0.1298-0.02960.01661.57770.67382.3533-0.0057-0.0320.0223-0.04060.04330.1357-0.2263-0.3592-0.03750.13530.05750.01180.21070.02810.1748-10.66627.88415.7864
60.11120.4131-0.11911.24180.17710.78360.0511-0.0255-0.00290.18860.009-0.0063-0.0751-0.0604-0.06010.19860.02820.03990.1723-0.01280.1329-1.330430.01132.6894
7-1.9655-1.38960.40342.47522.01333.7170.252-0.14930.45351.3984-0.1967-0.44560.2809-0.3039-0.05530.7158-0.0636-0.0114-0.0234-0.01580.0403-5.349921.377938.7486
82.8217-1.7688-1.1574.66510.39315.63370.1189-0.2027-0.04220.2697-0.0936-0.16250.3820.436-0.02530.22510.0283-0.05310.16670.0510.1416.3358.503933.2519
90.23180.7837-0.31291.7269-0.04480.96890.0855-0.05210.02870.2152-0.0427-0.12560.21140.0596-0.04280.21970.0030.00050.16830.02080.14531.60749.713429.4924
101.69861.426-0.9551.1201-0.97911.16840.0079-0.02760.0282-0.0819-0.006-0.01050.23050.0877-0.0020.20520.01450.04640.14810.00530.1688.215111.942517.0019
112.8393-2.565-0.15461.9630.14831.81350.0214-0.1736-0.1377-0.02780.07380.14420.15020.3346-0.09520.16860.00870.01670.26060.00350.1617.593622.517224.2252
121.1683-0.5534-0.84340.660.52252.24330.1005-0.150.0886-0.03020.0141-0.1823-0.26960.2875-0.11460.1022-0.04980.04980.2033-0.01930.215421.601232.175117.9184
13-1.62623.8928-0.4343-2.08384.68234.61970.538-0.45710.3723-0.3964-0.2611-0.0958-1.0730.0687-0.27690.337-0.20290.23280.0895-0.12680.238721.062840.649516.958
140.4448-0.4158-0.65161.97160.05611.28580.0505-0.07590.0529-0.17120.0502-0.1642-0.02030.2804-0.10060.1041-0.0080.08840.2217-0.0070.211126.680427.25558.3509
152.02370.5187-1.37171.70071.08243.9099-0.10890.19850.0098-0.12460.0119-0.0164-0.0956-0.15920.0970.1387-0.01150.06660.20430.00620.179513.353926.82867.0904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 47
2X-RAY DIFFRACTION2A48 - 83
3X-RAY DIFFRACTION3A84 - 101
4X-RAY DIFFRACTION4A102 - 119
5X-RAY DIFFRACTION5A120 - 159
6X-RAY DIFFRACTION6A160 - 213
7X-RAY DIFFRACTION7A214 - 226
8X-RAY DIFFRACTION8A227 - 251
9X-RAY DIFFRACTION9A252 - 280
10X-RAY DIFFRACTION10A281 - 315
11X-RAY DIFFRACTION11A316 - 333
12X-RAY DIFFRACTION12A342 - 378
13X-RAY DIFFRACTION13A379 - 391
14X-RAY DIFFRACTION14A392 - 418
15X-RAY DIFFRACTION15A419 - 434

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