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- PDB-4uqf: CRYSTAL STRUCTURE OF LISTERIA MONOCYTOGENES GTP CYCLOHYDROLASE I -

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Basic information

Entry
Database: PDB / ID: 4uqf
TitleCRYSTAL STRUCTURE OF LISTERIA MONOCYTOGENES GTP CYCLOHYDROLASE I
ComponentsGTP cyclohydrolase 1
KeywordsHYDROLASE / FOLIC ACID BIOSYNTHESIS / ALLOSTERIC ENZYME
Function / homology
Function and homology information


: / GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / zinc ion binding / cytoplasm
Similarity search - Function
GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 ...GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GTP cyclohydrolase 1 / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchuessler, S. / Perbandt, M. / Fischer, M. / Graewert, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structure of GTP cyclohydrolase I from Listeria monocytogenes, a potential anti-infective drug target.
Authors: Schussler, S. / Haase, I. / Perbandt, M. / Illarionov, B. / Siemens, A. / Richter, K. / Bacher, A. / Fischer, M. / Grawert, T.
History
DepositionJun 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 18, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
F: GTP cyclohydrolase 1
G: GTP cyclohydrolase 1
H: GTP cyclohydrolase 1
I: GTP cyclohydrolase 1
J: GTP cyclohydrolase 1


Theoretical massNumber of molelcules
Total (without water)229,16510
Polymers229,16510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44150 Å2
ΔGint-274.8 kcal/mol
Surface area60140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.249, 141.847, 90.776
Angle α, β, γ (deg.)90.00, 104.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GTP cyclohydrolase 1 / GTP cyclohydrolase I / GTP-CH-I


Mass: 22916.459 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND BETWEEN S78 AND S150 / Source: (gene. exp.) Listeria monocytogenes (bacteria) / Description: ATCC, LGC STANDARDS GMBH, WESEL, GERMANY / Gene: folE, B4Y57_10615, D3B94_12135, FORC68_1988 / Plasmid: PNCO113 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1BLUE
References: UniProt: A0A1D2IZD1, UniProt: Q8Y5X1*PLUS, GTP cyclohydrolase I

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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: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.3 / Details: 0.1 M HEPES PH 7.3, 1.33 M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2012 / Details: KB-MIRRORS
RadiationMonochromator: DOUBLE SILICON (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 74531 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FB1

1fb1


Resolution: 2.4→87.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 23.046 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.5 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22593 3752 5 %RANDOM
Rwork0.19245 ---
obs0.19415 70754 99.61 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.645 Å2
Baniso -1Baniso -2Baniso -3
1-6.08 Å20 Å2-3.5 Å2
2---2.66 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→87.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14475 0 0 0 14475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914718
X-RAY DIFFRACTIONr_bond_other_d0.010.0214707
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.97319854
X-RAY DIFFRACTIONr_angle_other_deg1.839333825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99151850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34423.788631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.325152768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.66615119
X-RAY DIFFRACTIONr_chiral_restr0.0950.22321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116273
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023114
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_it4.9362.8717430
X-RAY DIFFRACTIONr_mcbond_other4.9322.8717429
X-RAY DIFFRACTIONr_mcangle_it6.924.3019270
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.9153.5467288
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 281 -
Rwork0.309 5214 -
obs--99.8 %
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)
12.5239-0.1346-0.22720.42830.05150.59320.04220.0350.06490.0324-0.00330.00880.0684-0.0109-0.03890.0333-0.00340.05070.180200.134323.19120.6521.628
22.25051.57260.88641.82270.61240.5279-0.03310.1427-0.0085-0.14840.0048-0.11660.04860.09990.02830.05260.02950.06540.21150.02940.150540.07915.49-23.994
32.6305-1.93440.38341.7697-0.30750.34530.0407-0.0743-0.0307-0.0340.00980.09560.081-0.1043-0.05050.0413-0.02430.0390.2173-0.03450.153612.09713.925-22.739
40.56580.13861.06790.76171.21343.6624-0.05620.02430.0388-0.07920.0577-0.1194-0.1790.1141-0.00150.0469-0.01170.08210.1980.00480.195249.25343.287-35.041
51.7091-1.46430.48731.822-0.50290.59920.0216-0.0962-0.00350.09920.00730.0750.0292-0.1546-0.02890.05-0.02770.07240.2168-0.02420.174821.35851.5495.843
60.7723-0.59021.35811.4944-1.59893.2129-0.0539-0.05990.08820.0367-0.00460.1166-0.0855-0.14850.05860.0306-0.00140.06120.2182-0.03480.21590.81336.865-4.798
72.97240.5249-0.51820.3512-0.16260.55360.02790.0575-0.0501-0.11340.03430.03320.1249-0.0151-0.06220.1143-0.01090.0410.2133-0.00160.156228.43627.293-45.522
80.3072-0.16110.92360.7483-0.93373.4595-0.03510.01240.0592-0.0559-0.00930.0182-0.02830.0230.04440.0402-0.00850.04240.16440.00240.183537.46965.385-16.459
90.5897-0.0270.63780.48481.02293.8694-0.03290.03390.1847-0.05110.03260.0659-0.2096-0.1410.00030.06670.0240.03350.21920.05050.268210.45564.236-17.267
102.14822.09461.11632.81260.77171.1411-0.10350.1873-0.0901-0.33530.0741-0.0557-0.05110.13010.02930.11890.03460.03840.19210.03610.192427.42458.209-42.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 188
2X-RAY DIFFRACTION2B3 - 188
3X-RAY DIFFRACTION3C3 - 188
4X-RAY DIFFRACTION4D3 - 188
5X-RAY DIFFRACTION5E3 - 188
6X-RAY DIFFRACTION6F3 - 188
7X-RAY DIFFRACTION7G3 - 188
8X-RAY DIFFRACTION8H3 - 188
9X-RAY DIFFRACTION9I3 - 188
10X-RAY DIFFRACTION10J3 - 188

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