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- PDB-1o4v: Crystal structure of the catalytic subunit of a phosphoribosylami... -

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Entry
Database: PDB / ID: 1o4v
TitleCrystal structure of the catalytic subunit of a phosphoribosylaminoimidazole mutase (tm0446) from thermotoga maritima at 1.77 A resolution
Componentsphosphoribosylaminoimidazole mutase PurE
KeywordsLYASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
: / Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77 A resolution
Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. ...Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJul 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_special_symmetry
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphoribosylaminoimidazole mutase PurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2623
Polymers20,0701
Non-polymers1922
Water2,126118
1
A: phosphoribosylaminoimidazole mutase PurE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)162,09924
Polymers160,5628
Non-polymers1,53716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area36850 Å2
ΔGint-444 kcal/mol
Surface area41350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.249, 103.249, 65.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

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Components

#1: Protein phosphoribosylaminoimidazole mutase PurE / AIR carboxylase / AIRC


Mass: 20070.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: PURE OR TM0446 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYS7, phosphoribosylaminoimidazole carboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.18 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6
Details: 2M ammonium sulfate, 0.1M tri-sodium citrate dihydrate pH 5.6, 0.2M potassium sodium tartrate tetrahydrate , VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
418 mg/mlprotein1drop
52.0 Mammonium sulfate1reservoir
60.2 Msodium potassium tartrate1reservoir
70.1 MTris1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.95369
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2003 / Details: flat mirror
RadiationMonochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.77→24.37 Å / Num. all: 16697 / Num. obs: 16697 / % possible obs: 95.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 34.3 Å2 / Rsym value: 0.072 / Net I/σ(I): 19.3
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 931 / Rsym value: 0.452 / % possible all: 73.8
Reflection
*PLUS
Highest resolution: 1.77 Å / Num. obs: 16698 / Num. measured all: 119908 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 73.8 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QCZ

1qcz


Resolution: 1.77→24.37 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.354 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. WEAK, AMBIGUOUS DENSITY FOR BOTH THE N- AND C-TERMINAL RESIDUES WAS NOT MODELED. 2. UNEXPLAINED SURFACE DENSITY BETWEEN ASP11 AND ARG40, AND AT THE INTER-OCTAMER CONTACT AROUND GLU145, ...Details: 1. WEAK, AMBIGUOUS DENSITY FOR BOTH THE N- AND C-TERMINAL RESIDUES WAS NOT MODELED. 2. UNEXPLAINED SURFACE DENSITY BETWEEN ASP11 AND ARG40, AND AT THE INTER-OCTAMER CONTACT AROUND GLU145, WAS MODELED AS WATERS. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18177 838 5 %RANDOM
Rwork0.14981 ---
obs0.1514 15859 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.807 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20 Å2
2---2.05 Å20 Å2
3---4.11 Å2
Refinement stepCycle: LAST / Resolution: 1.77→24.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 10 118 1408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221330
X-RAY DIFFRACTIONr_bond_other_d0.0060.021280
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9731795
X-RAY DIFFRACTIONr_angle_other_deg0.92732974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2455168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01223.77453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6941510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.2230.2254
X-RAY DIFFRACTIONr_nbd_other0.1760.21246
X-RAY DIFFRACTIONr_nbtor_other0.0850.2805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.218
X-RAY DIFFRACTIONr_mcbond_it0.8731.5839
X-RAY DIFFRACTIONr_mcangle_it1.58921354
X-RAY DIFFRACTIONr_scbond_it2.6843491
X-RAY DIFFRACTIONr_scangle_it4.5444.5441
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 46 4.94 %
Rwork0.234 885 -
Refinement TLS params.Method: refined / Origin x: 23.771 Å / Origin y: 1.379 Å / Origin z: 9.73 Å
111213212223313233
T-0.0434 Å20.0012 Å2-0.0297 Å2--0.007 Å20.0101 Å2---0.1488 Å2
L0.347 °20.0849 °2-0.1008 °2-2.1185 °2-0.2685 °2--0.3698 °2
S0.0036 Å °-0.1358 Å °-0.029 Å °0.2385 Å °-0.0159 Å °-0.1804 Å °-0.0321 Å °0.0959 Å °0.0123 Å °
Refinement TLS groupSelection: ALL
Software
*PLUS
Name: REFMAC / Version: 5.1.9999 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16697 / % reflection Rfree: 5 % / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.46
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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