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- PDB-5vev: Crystal Structure of Phosphoribosylamine-glycine Ligase from Neis... -

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Basic information

Entry
Database: PDB / ID: 5vev
TitleCrystal Structure of Phosphoribosylamine-glycine Ligase from Neisseria gonorrhoeae
ComponentsPhosphoribosylamine--glycine ligase
KeywordsLIGASE / SSGCID / Neisseria gonorrhoeae / Phosphoribosylamine--glycine ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleobase biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylglycinamide synthetase, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. ...Phosphoribosylglycinamide synthetase, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Phosphoribosylamine--glycine ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Phosphoribosylamine-glycine Ligase from Neisseria gonorrhoeae
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylamine--glycine ligase
B: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,82723
Polymers92,5092
Non-polymers1,31821
Water9,836546
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A: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,92612
Polymers46,2541
Non-polymers67211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-4 kcal/mol
Surface area17060 Å2
MethodPISA
2
B: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,90111
Polymers46,2541
Non-polymers64710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-12 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.310, 99.450, 131.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoribosylamine--glycine ligase / GARS / Glycinamide ribonucleotide synthetase / Phosphoribosylglycinamide synthetase


Mass: 46254.434 Da / Num. of mol.: 2 / Mutation: R211Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: purD, NGK_2312 / Plasmid: NegoA.00865.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B4RPN9, phosphoribosylamine-glycine ligase

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Non-polymers , 5 types, 567 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1:1 15 mg/mL NegoA.00865.a.B1.PW37919 / JCSG+(d4) (30% w/v PEG8000, 0.1 M sodium acetate/acetic acid, pH 4.5, 0.2 M lithium sulfate), cryoprotectant: 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2017 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→46.515 Å / Num. obs: 74874 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6.283 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.061 / Χ2: 1.015 / Net I/σ(I): 19.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.956.3820.5163.6854000.8870.56297.2
1.95-26.3990.4024.6853040.9270.43897.4
2-2.066.3950.3136.0151850.9530.34197.3
2.06-2.126.3810.2497.3250090.9670.27297.5
2.12-2.196.3620.28.9948760.980.21897.7
2.19-2.276.3440.1710.4547430.9850.18597.8
2.27-2.366.3480.13412.8245780.990.14797.9
2.36-2.456.3330.11614.5544130.9920.12797.9
2.45-2.566.3290.09617.3242410.9940.10598
2.56-2.696.3140.08219.5440910.9960.0998.1
2.69-2.836.2910.06723.1138680.9970.07398.4
2.83-36.2680.05627.4136960.9970.06198.4
3-3.216.210.04831.5734740.9980.05398.6
3.21-3.476.2050.04136.532370.9980.04598.4
3.47-3.86.1570.03839.4829950.9980.04198.5
3.8-4.256.1110.03542.0127290.9980.03898.6
4.25-4.916.0630.03144.0224460.9990.03498.7
4.91-6.016.0060.03242.5420670.9980.03598.8
6.01-8.55.9130.03143.2416370.9980.03498.3
8.5-46.5155.5680.02944.578850.9990.03289.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MJF

3mjf


Resolution: 1.9→46.515 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 2062 2.76 %
Rwork0.1657 72763 -
obs0.1667 74825 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.25 Å2 / Biso mean: 41.8728 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 1.9→46.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5962 0 81 552 6595
Biso mean--65.32 43.05 -
Num. residues----813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066205
X-RAY DIFFRACTIONf_angle_d0.8268436
X-RAY DIFFRACTIONf_chiral_restr0.054970
X-RAY DIFFRACTIONf_plane_restr0.0051115
X-RAY DIFFRACTIONf_dihedral_angle_d13.9523696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94420.25541460.21824711485797
1.9442-1.99280.23331350.20094781491697
1.9928-2.04670.22341420.18834741488398
2.0467-2.10690.22811210.18154799492098
2.1069-2.17490.23691360.18354797493398
2.1749-2.25270.21941470.18574795494298
2.2527-2.34280.2141250.17744807493298
2.3428-2.44950.221170.17764849496698
2.4495-2.57860.19781310.1774849498098
2.5786-2.74010.20341240.18254874499898
2.7401-2.95170.21791610.1854874503599
2.9517-3.24860.21161590.17844853501299
3.2486-3.71860.17161320.15414933506598
3.7186-4.68430.18311480.13084983513199
4.6843-46.52920.18221380.15485117525597
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)
11.99240.313-0.68832.5007-0.20783.92640.1677-0.2574-0.05640.5625-0.08380.15920.1108-0.2768-0.09220.3074-0.06450.02180.20820.01680.1522-9.339110.774749.2857
23.69181.1607-1.02641.14060.24420.27280.3864-0.6265-0.58440.0522-0.3326-0.45580.23610.724-0.0870.2980.0723-0.09520.63790.03960.542124.22311.524534.5272
31.0230.29260.20232.10820.04651.95390.07250.0324-0.00810.2528-0.0299-0.2236-0.09750.1828-0.05760.1555-0.0255-0.02320.12550.00050.18012.28113.10633.8359
41.37041.14090.21561.15110.89143.80080.5274-0.55010.56471.0828-0.45650.467-1.3046-0.31130.17760.9677-0.14510.08940.2971-0.14030.3201-0.278231.089852.2494
53.96331.33772.42074.27850.42953.66230.00640.06210.15110.2027-0.0779-0.1596-0.57420.28020.06350.3774-0.0690.01310.13070.00870.26556.357631.658337.5638
61.94220.47310.79713.70180.81435.54640.1090.2549-0.0172-0.39060.0174-0.0615-0.09390.2903-0.12090.2315-0.0109-0.05270.27-0.02470.1615-9.66283.6469-0.9374
74.1083-1.41480.25850.3666-0.6158-0.18730.4140.4874-0.64680.0779-0.6040.42050.1039-0.31880.15650.2836-0.0493-0.0030.8511-0.24070.6096-43.4915-1.392814.9641
81.16190.2275-0.02831.76190.78344.5531-0.09430.10570.2472-0.4362-0.05370.3722-0.7602-0.9921-0.0060.30310.1592-0.14620.38390.00520.3139-21.461114.36238.6425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 102 )A-1 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 190 )A103 - 190
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 345 )A191 - 345
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 379 )A346 - 379
5X-RAY DIFFRACTION5chain 'A' and (resid 380 through 423 )A380 - 423
6X-RAY DIFFRACTION6chain 'B' and (resid -2 through 102 )B-2 - 102
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 190 )B103 - 190
8X-RAY DIFFRACTION8chain 'B' and (resid 191 through 421 )B191 - 421

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