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- PDB-3lp8: Crystal structure of phosphoribosylamine-glycine ligase from Ehrl... -

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Basic information

Entry
Database: PDB / ID: 3lp8
TitleCrystal structure of phosphoribosylamine-glycine ligase from Ehrlichia chaffeensis
ComponentsPhosphoribosylamine-glycine ligase
KeywordsLIGASE / SSGCID / NIH / NIAID / SBRI / UW / emerald biostructures / ALS collaborative crystallography / Ehrlichia chaffeensis / phosphoribosylamine-glycine ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


purine nucleobase biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / '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 / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / 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
PHOSPHATE ION / Phosphoribosylamine--glycine ligase
Similarity search - Component
Biological speciesEhrlichia chaffeensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of phosphoribosylamine-glycine ligase from Ehrlichia chaffeensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Davies, D. / Staker, B.
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 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_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_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

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Assembly

Deposited unit
A: Phosphoribosylamine-glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5477
Polymers48,4521
Non-polymers956
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.850, 74.160, 107.290
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 Phosphoribosylamine-glycine ligase


Mass: 48451.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis (bacteria) / Strain: Arkansas / Gene: purD, ECH_1006 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2GFJ0, phosphoribosylamine-glycine ligase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: HR INDEX SCREEN F2: 100MM TRIS PH 8.5, 20% PEG 2000 MME, 200MM TRIMETHYLAMINE-N-OXIDE; EHCHA.00685.A AT 22.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 22362 / Num. obs: 21857 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 31.38 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.53
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1607 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb deposition 2ys7 modified with CCP4 program CHAINSAW

2ys7


Resolution: 2.15→43.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.334 / SU ML: 0.121 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1128 5.2 %RANDOM
Rwork0.17 ---
all0.172 22362 --
obs0.172 21807 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.14 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 10 222 3420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223254
X-RAY DIFFRACTIONr_bond_other_d0.0020.022144
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9684416
X-RAY DIFFRACTIONr_angle_other_deg0.86635274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81224.887133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61315547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2821513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213658
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
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_it0.6181.52088
X-RAY DIFFRACTIONr_mcbond_other0.1541.5869
X-RAY DIFFRACTIONr_mcangle_it1.18823346
X-RAY DIFFRACTIONr_scbond_it2.15731166
X-RAY DIFFRACTIONr_scangle_it3.5044.51067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 80 -
Rwork0.207 1270 -
obs--84.22 %
Refinement TLS params.Method: refined / Origin x: 9.976 Å / Origin y: 0.219 Å / Origin z: 12.214 Å
111213212223313233
T0.0049 Å20.0077 Å20.0037 Å2-0.0644 Å2-0.0158 Å2--0.1239 Å2
L1.1945 °2-0.1674 °2-0.3317 °2-0.7791 °20.1352 °2--0.9396 °2
S0.0021 Å °-0.0806 Å °0.0406 Å °-0.0206 Å °0.0013 Å °0.0047 Å °0.0111 Å °0.0782 Å °-0.0034 Å °

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