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- PDB-4du6: Crystal structure of GTP cyclohydrolase I from Yersinia pestis co... -

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Basic information

Entry
Database: PDB / ID: 4du6
TitleCrystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP
ComponentsGTP cyclohydrolase 1
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold
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
GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / GTP cyclohydrolase 1 / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.106 Å
AuthorsMaltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Source and taxonomy
Revision 1.2Sep 13, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,96224
Polymers125,1095
Non-polymers3,85319
Water3,279182
1
A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
hetero molecules

A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,92448
Polymers250,21710
Non-polymers7,70738
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area69500 Å2
ΔGint-228 kcal/mol
Surface area67680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.047, 104.912, 70.070
Angle α, β, γ (deg.)90.00, 96.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-404-

HOH

Details-x+1,y,-z is applied to the asymmetric unit (pentamer) to generate decamer.

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
GTP cyclohydrolase 1 / GTP cyclohydrolase I


Mass: 25021.715 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: folE, YPTB1520 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q66C86, UniProt: Q8ZG15*PLUS, GTP cyclohydrolase I

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Non-polymers , 6 types, 201 molecules

#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M Lithium Chloride; 0.1M TRIS HCl pH 8.5; 8% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.106→50 Å / Num. all: 70010 / Num. obs: 70010 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 37.55 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2881 / Rsym value: 0.482 / % possible all: 80.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GTP

1gtp


Resolution: 2.106→43.198 Å / SU ML: 0.27 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3519 5.05 %random
Rwork0.18 ---
all0.182 69649 --
obs0.182 69649 96.32 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.745 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 57.1 Å2
Baniso -1Baniso -2Baniso -3
1--17.3027 Å2-0 Å2-1.0167 Å2
2---5.871 Å20 Å2
3---23.1737 Å2
Refinement stepCycle: LAST / Resolution: 2.106→43.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8535 0 236 182 8953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139122
X-RAY DIFFRACTIONf_angle_d1.48212398
X-RAY DIFFRACTIONf_dihedral_angle_d183475
X-RAY DIFFRACTIONf_chiral_restr0.1011476
X-RAY DIFFRACTIONf_plane_restr0.0061563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1058-2.13470.341930.28182004209772
2.1347-2.16510.32141100.25412283239384
2.1651-2.19750.2531390.24722295243485
2.1975-2.23180.31361380.24192397253588
2.2318-2.26840.31741410.23442550269193
2.2684-2.30750.30771490.22912629277896
2.3075-2.34950.25751580.22352676283499
2.3495-2.39460.26631460.20292705285199
2.3946-2.44350.25571450.21692720286599
2.4435-2.49660.25511440.21532724286899
2.4966-2.55470.28071330.21252699283299
2.5547-2.61860.24391520.20852688284099
2.6186-2.68940.29091700.20862746291699
2.6894-2.76850.29341360.206626892825100
2.7685-2.85780.27651290.20292756288599
2.8578-2.960.26861450.227172862100
2.96-3.07850.22041330.200327812914100
3.0785-3.21850.27641500.18927132863100
3.2185-3.38810.23361230.18327752898100
3.3881-3.60030.23751420.171227392881100
3.6003-3.87810.21371450.167227492894100
3.8781-4.26810.19191500.141727552905100
4.2681-4.8850.15851540.129227572911100
4.885-6.15170.20941480.174427742922100
6.1517-43.20680.1691460.16232809295599
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)
14.633-1.0917-1.78447.9198-1.71045.76630.0610.54630.068-0.585-0.1649-1.4159-0.04931.0472-0.00050.3599-0.10550.14590.8141-0.03620.6108127.9851-6.0771-18.0341
23.15311.48012.96132.33661.5923.1014-0.16610.1214-0.191-0.18320.2281-0.2613-0.23260.819-0.03480.4024-0.1467-0.07220.64120.10560.7401132.36788.05770.9285
32.6018-1.6763-1.32191.54020.10951.8761-0.0934-1.1435-0.32090.4524-0.0186-0.25890.13060.21260.05880.6035-0.1421-0.24790.79890.05440.6583124.583712.025519.779
41.57452.48082.01157.1148.29912.0946-0.0963-0.0091-0.08710.3928-0.1565-0.07470.52350.39940.37960.3996-0.027900.52680.09620.6068125.92151.22191.8644
53.36451.81371.34134.95281.872.6528-0.04720.1957-0.1495-0.10570.0457-0.20970.07360.27450.02510.2427-0.04020.06410.42220.02690.3208112.8894-6.32-11.9459
61.0998-0.847-0.29912.04361.68132.196-0.03670.18640.2487-0.16390.0497-0.2043-0.16490.18820.01350.3115-0.08950.05150.40370.05810.4163110.35024.0653-14.1244
72.07631.1180.12622.09242.77552.02390.0262-0.09661.23220.4485-0.38610.878-0.0591-1.04510.46630.5187-0.03450.06850.5797-0.0720.670798.5316-1.4772-20.5495
86.63822.3508-1.2333.4134-2.34726.7882-0.02460.4705-1.1398-0.6549-0.0506-0.08060.84610.4418-0.05770.53610.05860.04130.4771-0.24470.629695.1638-38.3096-21.707
92.3526-1.38212.52019.534-6.77882.02530.60490.48110.0094-0.7333-0.8239-0.83081.44010.36550.1450.79030.09570.10790.702-0.19460.8437105.9894-40.1717-13.7336
105.70332.29795.25064.39651.33828.7445-0.12020.1546-0.44120.30620.00370.2020.93990.52530.07730.42640.14720.06530.3734-0.0010.6254109.661-40.39295.0066
113.89991.76832.73574.80050.05065.61790.2859-0.7752-0.52530.7458-0.06650.04180.208-0.0782-0.22410.46620.1308-0.01140.55510.05110.5194109.5793-33.133217.3189
124.896-0.75356.80940.62370.15142.04780.159-0.1901-0.42810.05290.0255-0.00730.7426-0.384-0.11390.3924-0.00250.06810.3031-0.01870.544499.8712-36.1488-1.0458
137.8163-0.88144.02132.9188-1.13844.79390.26460.2829-0.8736-0.67860.31981.0670.7124-0.7687-0.60180.436-0.1029-0.02510.6109-0.08210.551578.6741-27.0369-22.5488
147.2866-1.44164.08651.287-1.23264.6910.01210.111-0.4726-0.06230.1593-0.02390.1635-0.1198-0.17580.2855-0.02850.06950.2557-0.0240.322393.2211-21.9539-12.3919
152.36750.22731.28680.9220.30772.44530.00690.2361-0.2481-0.10910.0147-0.05690.1750.256-0.0270.2866-0.00850.08290.2888-0.03490.344297.3929-21.1806-14.4301
162.0345-1.3564-0.56947.4485-1.28578.59690.0335-0.06091.57770.3853-0.3833-0.2383-1.1417-0.10450.37040.3586-0.05430.00430.491-0.10120.559890.1678-8.7744-23.6535
172.0186-5.3303-4.72787.51923.28937.08270.09661.6026-0.9701-0.1574-0.65081.48970.6109-1.87610.53010.4698-0.0996-0.11120.8946-0.17850.72554.5687-16.7978-26.3002
182.00065.6354-9.10694.3306-5.95188.4385-1.18390.6602-1.6097-0.54180.2947-0.63151.16-1.45230.81070.5593-0.2058-0.02360.9058-0.02020.79256.0285-28.0887-19.4852
195.1118-2.77773.68223.6452-1.30484.63030.1156-0.3788-0.14880.1421-0.11060.61510.3475-0.5485-0.01280.3477-0.15120.05360.46260.01570.521855.2642-34.1857-1.037
205.7679-2.12081.0684.40050.03154.3717-0.4219-1.0956-0.31970.53680.4520.95650.4137-0.56810.0680.4125-0.06150.09980.58460.10980.593461.0026-32.998911.8033
211.7669-1.16192.26673.1974-3.34997.4883-0.18070.05-0.0434-0.0373-0.01140.20450.1416-1.01050.18960.28-0.06040.0050.524-0.05480.528756.5783-22.6974-5.8899
222.86050.63230.05366.0474-2.02453.0344-0.07870.37030.2595-0.23790.05970.5303-0.2081-0.43570.03290.25340.0155-0.02450.4209-0.03250.361264.8591-7.7545-17.6219
233.755-2.24914.31553.6289-4.59858.2480.06630.2905-0.2634-0.25460.0340.18970.14530.0823-0.09420.2241-0.00520.01540.2877-0.0780.290373.622-14.8986-18.3122
242.04051.21050.6182.0571.41382.0179-0.2807-0.04560.54540.4988-0.1742-0.877-0.22911.09790.5440.52250.0321-0.12510.50690.06330.582281.2144-2.6551-23.067
254.3714-0.78260.1828.59662.10734.67480.10210.49991.18640.0023-0.09620.0305-0.8316-0.733-0.07180.87610.2399-0.13870.68160.19650.826662.176928.7256-25.3575
269.6016-8.4028-9.34069.4627.29469.37770.54141.59670.70530.0157-0.78880.788-0.6553-1.46330.21630.62940.1617-0.08580.8258-0.02460.866751.013923.3408-19.3723
275.19070.0665-3.18120.72660.23212.91070.1140.02460.6107-0.1166-0.04960.1793-0.4853-0.1194-0.05590.44050.0998-0.14250.39660.01790.555561.84320.0455-8.8304
281.4810.4826-0.20841.8978-1.05821.7825-0.11850.2430.3982-0.08650.15670.1943-0.2885-0.2681-0.02650.44760.0781-0.10520.42980.04240.455869.085113.0969-17.6119
292.02291.7653-0.45549.497-3.44369.9622-0.3854-0.1286-1.41680.5171-0.5092-1.01670.57650.99710.9130.4367-0.02070.00580.4540.16240.702283.93388.1386-23.9703
302.83420.7014-0.17933.00581.29453.92490.00610.04860.9812-0.6967-0.0358-0.4463-1.50470.34180.07351.1446-0.1893-0.02740.55110.26041.0771104.467737.8388-18.3922
312.6325-0.0782-1.01123.71950.26791.562-0.16530.08840.2578-0.1968-0.19530.0783-0.62010.12520.20561.8703-0.0918-0.04750.4066-0.08781.275892.120547.29612.9955
326.6574-0.4905-0.4433.3561-1.40724.48120.4988-0.97131.36140.16480.0257-0.2143-1.47950.1959-0.50021.1665-0.045-0.03020.6452-0.26340.950385.550342.148414.6542
333.8063-1.6917-3.50511.57230.07465.7610.1991-0.4581.17280.00020.0143-0.4637-1.40410.9287-0.2010.972-0.2632-0.08270.4716-0.03940.950298.772437.501-1.1969
343.0163-1.1111-1.31697.41454.22114.9441-0.09670.20450.3157-0.04070.7627-1.3134-0.31150.9555-0.75280.5161-0.1970.01550.6797-0.00690.6372114.337916.5913-18.3893
354.3172-2.1324-2.45624.0432.06163.86610.10640.13020.3889-0.04890.0481-0.0779-0.46810.1503-0.10360.4396-0.1059-0.02070.32460.08230.462797.908921.5854-11.9422
362.1801-0.0563-0.34452.06140.82271.9744-0.05780.09870.4777-0.2142-0.129-0.4354-0.63910.31970.2040.5908-0.1411-0.0380.36220.13760.6347100.57626.165-14.1894
379.2258-3.348-7.88092.96653.34258.68310.09380.59710.4479-0.0731-0.1565-0.2019-0.6201-0.30270.08370.4273-0.0351-0.08770.31910.11520.480691.690521.6998-13.5165
389.8195-1.0016-7.41952.04240.52077.02170.25070.34940.8533-0.21850.0885-0.1379-0.5943-0.1624-0.33380.5083-0.0569-0.10930.33240.08640.475887.1119.6325-15.73
399.60330.3964-4.77372.0399-1.33332.0178-0.33040.2559-1.39490.2138-0.47360.54430.7245-0.48860.88490.4951-0.070.0920.55860.01190.623394.94277.8909-22.7284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:18)
2X-RAY DIFFRACTION2chain 'A' and (resseq 19:49)
3X-RAY DIFFRACTION3chain 'A' and (resseq 50:60)
4X-RAY DIFFRACTION4chain 'A' and (resseq 61:81)
5X-RAY DIFFRACTION5chain 'A' and (resseq 82:149)
6X-RAY DIFFRACTION6chain 'A' and (resseq 150:205)
7X-RAY DIFFRACTION7chain 'A' and (resseq 206:220)
8X-RAY DIFFRACTION8chain 'B' and (resseq 2:18)
9X-RAY DIFFRACTION9chain 'B' and (resseq 19:30)
10X-RAY DIFFRACTION10chain 'B' and (resseq 31:48)
11X-RAY DIFFRACTION11chain 'B' and (resseq 49:60)
12X-RAY DIFFRACTION12chain 'B' and (resseq 61:81)
13X-RAY DIFFRACTION13chain 'B' and (resseq 82:97)
14X-RAY DIFFRACTION14chain 'B' and (resseq 98:132)
15X-RAY DIFFRACTION15chain 'B' and (resseq 133:205)
16X-RAY DIFFRACTION16chain 'B' and (resseq 206:217)
17X-RAY DIFFRACTION17chain 'C' and (resseq 2:18)
18X-RAY DIFFRACTION18chain 'C' and (resseq 19:30)
19X-RAY DIFFRACTION19chain 'C' and (resseq 31:48)
20X-RAY DIFFRACTION20chain 'C' and (resseq 49:60)
21X-RAY DIFFRACTION21chain 'C' and (resseq 61:81)
22X-RAY DIFFRACTION22chain 'C' and (resseq 82:149)
23X-RAY DIFFRACTION23chain 'C' and (resseq 150:205)
24X-RAY DIFFRACTION24chain 'C' and (resseq 206:220)
25X-RAY DIFFRACTION25chain 'D' and (resseq 2:18)
26X-RAY DIFFRACTION26chain 'D' and (resseq 19:30)
27X-RAY DIFFRACTION27chain 'D' and (resseq 31:132)
28X-RAY DIFFRACTION28chain 'D' and (resseq 133:205)
29X-RAY DIFFRACTION29chain 'D' and (resseq 206:217)
30X-RAY DIFFRACTION30chain 'E' and (resseq 2:30)
31X-RAY DIFFRACTION31chain 'E' and (resseq 31:48)
32X-RAY DIFFRACTION32chain 'E' and (resseq 49:60)
33X-RAY DIFFRACTION33chain 'E' and (resseq 61:81)
34X-RAY DIFFRACTION34chain 'E' and (resseq 82:97)
35X-RAY DIFFRACTION35chain 'E' and (resseq 98:132)
36X-RAY DIFFRACTION36chain 'E' and (resseq 133:165)
37X-RAY DIFFRACTION37chain 'E' and (resseq 166:182)
38X-RAY DIFFRACTION38chain 'E' and (resseq 183:205)
39X-RAY DIFFRACTION39chain 'E' and (resseq 206:218)

+
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