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Basic information

Entry
Database: PDB / ID: 1zcz
TitleCrystal structure of Phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase (TM1249) from THERMOTOGA MARITIMA at 1.88 A resolution
ComponentsBifunctional purine biosynthesis protein purH
KeywordsTRANSFERASE/HYDROLASE / TM1249 / Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) / IMP cyclohydrolase (EC 3.5.4.10) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI / TRANSFERASE-HYDROLASE COMPLEX
Function / homology
Function and homology information


phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / cytosol
Similarity search - Function
AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain ...AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Bifunctional purine biosynthesis protein PurH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution.
Authors: Axelrod, H.L. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Elsliger, M.A. / Abdubek, P. / Ambing, E. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / Duan, L. / Feuerhelm, J. / ...Authors: Axelrod, H.L. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Elsliger, M.A. / Abdubek, P. / Ambing, E. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / Duan, L. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C.L. / van den Bedem, H. / Weekes, D. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionApr 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional purine biosynthesis protein purH
B: Bifunctional purine biosynthesis protein purH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2526
Polymers102,7862
Non-polymers4674
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-45 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.084, 58.630, 72.749
Angle α, β, γ (deg.)99.26, 96.89, 106.13
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASPASPAA2 - 16614 - 178
21LYSLYSASPASPBB2 - 16614 - 178
12LEULEUHISHISAA167 - 452179 - 464
22LEULEUHISHISBB167 - 452179 - 464

NCS ensembles :
ID
1
2

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Components

#1: Protein Bifunctional purine biosynthesis protein purH / Phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase


Mass: 51392.867 Da / Num. of mol.: 2 / Mutation: 2.1.2.3, 3.5.4.10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: purH / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0X6
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.3 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 20.0% PEG-6000, 0.1M Citrate pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2005 / Details: Single crystal, cylindrically bent, Si(220)
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 74289 / % possible obs: 95.6 % / Redundancy: 2.9 % / Rsym value: 0.056 / Χ2: 0.962 / Net I/σ(I): 25.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Mean I/σ(I) obsNum. measured obsRsym valueΧ2% possible all
1.88-1.9170.61.60.020527370.3140.90570.6
1.91-1.9587.31.534080.2580.909
1.95-1.9893.61.636030.2210.925
1.98-2.0395.31.637080.1720.92
2.03-2.0796.21.737730.1450.957
2.07-2.1296.21.936750.1280.909
2.12-2.1797.1237890.130.97
2.17-2.23972.137970.1390.917
2.23-2.2997.12.237700.150.993
2.29-2.3797.42.337700.1690.953
2.37-2.4597.62.537840.1880.96
2.45-2.5597.82.838000.1680.917
2.55-2.67983.138270.1660.953
2.67-2.8198.13.538140.1380.949
2.81-2.9898.3438090.1141.003
2.98-3.2198.64.438290.081.01
3.21-3.5498.74.437990.0540.997
3.54-4.0599.14.438830.0431.006
4.05-5.199.24.438540.0350.918
5.1-5099.44.438600.0330.93

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT1.6data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1m9n 1g8mA

1m9n


Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.959 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). ELECTRON DENSITY INDICATES A CIS-PEPTIDE BOND CONFORMATION BETWEEN RESIDUES 355 AND 356 ON THE A AND B CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3700 5 %RANDOM
Rwork0.156 ---
all0.158 ---
obs0.15849 69797 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.497 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0.09 Å2-1.16 Å2
2--0.21 Å2-1.07 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6961 0 28 636 7625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227186
X-RAY DIFFRACTIONr_bond_other_d0.0050.026694
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9699722
X-RAY DIFFRACTIONr_angle_other_deg0.985315552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02524.257303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86151229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2511538
X-RAY DIFFRACTIONr_chiral_restr0.0870.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027973
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021443
X-RAY DIFFRACTIONr_nbd_refined0.220.21433
X-RAY DIFFRACTIONr_nbd_other0.1780.26592
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23418
X-RAY DIFFRACTIONr_nbtor_other0.0840.24224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2505
X-RAY DIFFRACTIONr_metal_ion_refined0.2230.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.213
X-RAY DIFFRACTIONr_mcbond_it1.60334511
X-RAY DIFFRACTIONr_mcbond_other0.61531846
X-RAY DIFFRACTIONr_mcangle_it2.57757234
X-RAY DIFFRACTIONr_scbond_it4.29682698
X-RAY DIFFRACTIONr_scangle_it6.267112488
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12423medium positional0.470.5
24150medium positional0.570.5
12423medium thermal1.072
24150medium thermal0.882
LS refinement shellResolution: 1.882→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 168 -
Rwork0.217 3246 -
obs--73.74 %
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)
12.4616-0.50320.53252.786-1.03581.9179-0.0533-0.223-0.43110.35590.10310.05640.2338-0.1339-0.0498-0.09080.01740.0298-0.0840.0176-0.153413.654-17.056222.9795
22.5794-0.46080.39911.3201-0.12420.83630.0095-0.1478-0.04790.0663-0.00070.2415-0.0087-0.1241-0.0088-0.1624-0.00940.0383-0.1630.0061-0.2-20.39571.1171-5.9379
32.494-0.00421.11234.28681.70232.9846-0.1433-0.01780.45190.29020.3506-0.8557-0.37870.3327-0.2072-0.06120.0019-0.0191-0.0625-0.045-0.045522.81145.209721.6997
41.2391-0.09110.23780.97950.19252.2714-0.06550.12840.1168-0.1472-0.0151-0.0802-0.17810.10820.0806-0.1764-0.01080.0183-0.18120.0387-0.1748-1.09455.9959-20.6128
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 16614 - 178
22AA167 - 452179 - 464
33BB-1 - 16611 - 178
44BB167 - 452179 - 464

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