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- PDB-3qcz: Crystal structure of bifunctional folylpolyglutamate synthase/dih... -

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Basic information

Entry
Database: PDB / ID: 3qcz
TitleCrystal structure of bifunctional folylpolyglutamate synthase/dihydrofolate synthase with Mn, AMPPNP and L-Glutamate bound
ComponentsDihydrofolate synthase / folylpolyglutamate synthase
KeywordsLIGASE / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / folC / dihydrofolate synthetase-folylpolyglutamate synthetase / DHFS / AMPPNP / Mn / L-Glu
Function / homology
Function and homology information


dihydrofolate synthase activity / folic acid-containing compound biosynthetic process / tetrahydrofolylpolyglutamate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / ATP binding / metal ion binding / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GLUTAMIC ACID / : / Dihydrofolate synthase/folylpolyglutamate synthase / Dihydrofolate synthase/folylpolyglutamate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNocek, B. / Makowska-Grzyska, M. / Maltseva, N. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of bifunctional folylpolyglutamate synthase/dihydrofolate synthase with Mn, AMPPNP and L-Glutamate bound
Authors: Nocek, B. / Makowska-Grzyska, M. / Maltseva, N. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2013Group: Structure summary
Revision 1.3Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: Dihydrofolate synthase / folylpolyglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4436
Polymers47,5511
Non-polymers8925
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.861, 83.237, 126.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate synthase / folylpolyglutamate synthase


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: dedC, YPO2769 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: Q0WDC2, UniProt: A0A5P8YIK0*PLUS, tetrahydrofolate synthase

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 Sodium formate, pH 7.0, 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: Nov 14, 2010 / 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: 2→40 Å / Num. all: 46230 / Num. obs: 46066 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11
Reflection shellResolution: 2→2.03 Å / % possible all: 99.7

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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: 2→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.946 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19888 2313 5 %RANDOM
Rwork0.17108 ---
all0.182 45869 --
obs0.17247 43556 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.587 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2---0.98 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 54 205 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213204
X-RAY DIFFRACTIONr_bond_other_d0.0020.022103
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9724357
X-RAY DIFFRACTIONr_angle_other_deg1.04635123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87523.723137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61715503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5271523
X-RAY DIFFRACTIONr_chiral_restr0.1210.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
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_it1.241.52021
X-RAY DIFFRACTIONr_mcbond_other0.3741.5828
X-RAY DIFFRACTIONr_mcangle_it2.15723221
X-RAY DIFFRACTIONr_scbond_it3.32431183
X-RAY DIFFRACTIONr_scangle_it5.2524.51135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 171 -
Rwork0.284 3006 -
obs--93.97 %
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)
11.35020.10481.56734.9401-0.65835.5789-0.06040.38660.1039-0.0907-0.0439-0.0042-0.80270.18470.10430.29080.0032-0.06130.11960.07680.1524-7.06236.3343-0.1969
22.4321-1.304-0.57332.4981.89417.7744-0.1462-0.13650.08610.25810.11530.3597-1.0642-0.91830.03090.1460.28250.04010.20630.03850.166-16.571134.954716.237
30.27250.10640.21960.2812-0.04461.08150.00130.05090.01830.04760.05530.03730.0069-0.0569-0.05660.1605-0.00110.02140.16980.01070.1729-3.148218.937915.6723
40.9587-0.8493-0.31331.21020.13982.6881-0.13970.1555-0.1052-0.15830.19570.1113-0.4861-0.1411-0.0560.24410.0376-0.05240.16140.06060.1596-11.132131.05455.7181
5-0.2408-0.19020.2291.41680.06262.0189-0.0198-0.0154-0.00030.04970.06710.2049-0.1886-0.311-0.04730.13020.05360.03560.19560.0190.1951-11.068925.43717.4806
60.13140.55350.08931.51850.52970.64730.0958-0.08060.04090.3307-0.0183-0.03670.022-0.0148-0.07750.22920.01510.03360.1487-0.00510.1228-0.081823.515234.5953
70.88240.2516-0.04731.12710.36261.37560.0533-0.00510.09980.28720.0449-0.05160.26790.0144-0.09820.23020.0133-0.00960.13050.01970.1397-0.02719.407627.7729
80.89590.8077-1.03320.4498-0.36171.1784-0.0664-0.0191-0.0759-0.04170.1312-0.10370.18890.1447-0.06490.18010.02690.02520.1619-0.01540.205111.36412.661415.6772
92.5051-1.76020.88641.56810.5171.9270.1698-0.0383-0.07140.04550.13960.02380.11940.3162-0.30940.15030.0123-0.02390.2346-0.05690.169418.186122.134924.4419
101.0427-0.3586-0.79960.8610.72342.0089-0.0034-0.07550.11550.02750.151-0.2197-0.25060.3138-0.14770.0993-0.06060.04460.2078-0.07130.203422.632531.166718.2937
111.4267-0.8017-0.29291.4290.23862.48110.09930.02610.0599-0.24050.036-0.1458-0.2110.3212-0.13530.0793-0.07780.10090.1761-0.03960.205625.042131.756410.9543
122.82281.3360.67441.2689-0.98282.1069-0.1570.35350.20590.00330.26350.0373-0.1180.0946-0.10640.1265-0.05620.01640.23130.01610.171313.360226.88068.8484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 22
2X-RAY DIFFRACTION2A23 - 47
3X-RAY DIFFRACTION3A48 - 97
4X-RAY DIFFRACTION4A98 - 124
5X-RAY DIFFRACTION5A125 - 164
6X-RAY DIFFRACTION6A165 - 255
7X-RAY DIFFRACTION7A256 - 285
8X-RAY DIFFRACTION8A286 - 315
9X-RAY DIFFRACTION9A316 - 333
10X-RAY DIFFRACTION10A341 - 376
11X-RAY DIFFRACTION11A377 - 417
12X-RAY DIFFRACTION12A418 - 701

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