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- PDB-4r7t: Crystal structure of glucosamine-6-phosphate deaminase from Vibri... -

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Basic information

Entry
Database: PDB / ID: 4r7t
TitleCrystal structure of glucosamine-6-phosphate deaminase from Vibrio cholerae
ComponentsGlucosamine-6-phosphate deaminase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta fold / alpha beta alpha sandwich / deaminase / cytosol
Function / homology
Function and homology information


glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of glucosamine-6-phosphate deaminase from Vibrio cholerae
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
C: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0289
Polymers91,7813
Non-polymers2466
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-38 kcal/mol
Surface area33940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.359, 135.124, 86.001
Angle α, β, γ (deg.)90.00, 106.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glucosamine-6-phosphate deaminase / GlcN6P deaminase / GNPDA / Glucosamine-6-phosphate isomerase


Mass: 30593.791 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: N16961 / Gene: nagB, VC_A1025 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q9KKS5, glucosamine-6-phosphate deaminase

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Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M magnesium chloride, 0.1M HEPES pH7.5, 30% PEG 400, 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: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 47655 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 26.99 Å2 / Rsym value: 0.086 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.52 / Rsym value: 0.395 / % possible all: 80.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1750)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FS5

1fs5


Resolution: 2.1→38.65 Å / SU ML: 0.31 / Isotropic thermal model: mixed / σ(F): 1.35 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 2417 5.07 %
Rwork0.1994 --
obs0.2022 47353 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6223 0 13 185 6421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086526
X-RAY DIFFRACTIONf_angle_d1.0028866
X-RAY DIFFRACTIONf_dihedral_angle_d14.0792390
X-RAY DIFFRACTIONf_chiral_restr0.037994
X-RAY DIFFRACTIONf_plane_restr0.0051162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13450.3505960.27082125X-RAY DIFFRACTION75
2.1345-2.18090.34381290.26362498X-RAY DIFFRACTION88
2.1809-2.23160.29691520.25512605X-RAY DIFFRACTION92
2.2316-2.28740.29851450.23882689X-RAY DIFFRACTION97
2.2874-2.34920.30641360.24332744X-RAY DIFFRACTION97
2.3492-2.41840.30211530.22262727X-RAY DIFFRACTION97
2.4184-2.49640.30651550.21622720X-RAY DIFFRACTION97
2.4964-2.58560.25881350.20432769X-RAY DIFFRACTION97
2.5856-2.68910.27711580.2212721X-RAY DIFFRACTION96
2.6891-2.81150.27931490.21572702X-RAY DIFFRACTION97
2.8115-2.95960.29081500.21322715X-RAY DIFFRACTION97
2.9596-3.1450.27211350.20872735X-RAY DIFFRACTION96
3.145-3.38770.28851630.20452727X-RAY DIFFRACTION96
3.3877-3.72830.21721320.18262740X-RAY DIFFRACTION96
3.7283-4.26720.19441490.16612651X-RAY DIFFRACTION95
4.2672-5.3740.21041460.16192695X-RAY DIFFRACTION95
5.374-38.65610.20921340.17722661X-RAY DIFFRACTION92
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)
10.27890.0408-0.26171.45381.40367.11790.0984-0.09640.24130.03780.03880.21970.1239-0.5562-0.08340.16660.0180.04860.2702-0.03610.37977.9317-17.807520.8599
24.8204-0.62920.07262.8193-0.72631.1891-0.10480.093-0.2244-0.02930.04530.1763-0.0703-0.08010.0520.254-0.01-0.01350.2334-0.04780.248518.4082-29.721912.0322
32.72680.08040.3491.89691.38632.3050.0802-0.0432-0.07060.17470.0702-0.08020.10780.1797-0.12350.221-0.00420.00750.23270.00910.287930.651-22.421618.0063
41.1808-0.2304-0.71681.14850.87322.638-0.0208-0.0049-0.04670.0707-0.11510.16450.0539-0.21290.10590.1917-0.0018-0.01330.17740.00250.245415.7642-11.325329.5394
50.90261.27990.5062.01390.99664.30740.21030.0775-0.21290.11940.0947-0.22490.39850.3375-0.26790.19050.04020.00840.25020.050.341452.5708-7.627120.8596
63.5357-0.4289-0.14624.04031.85487.70880.0120.03060.41230.1027-0.1219-0.39880.4406-0.04360.19360.154-0.03980.050.17650.07250.312857.2214-0.61712.6208
71.6221-1.5283-0.00343.44420.99231.2886-0.0440.04920.08910.06140.1029-0.03790.07750.0032-0.00710.218-0.02880.04180.24510.01440.17756.14154.274510.6215
81.9431-1.8737-0.0523.17840.9781.12190.0370.07030.1936-0.14970.0032-0.1628-0.1562-0.0597-0.04380.2157-0.00060.04670.19930.02530.314958.052814.212811.949
91.3831-0.2443-1.2882.2319-1.06753.13730.13910.18330.121-0.27150.0640.071-0.0164-0.2539-0.20980.208-0.0186-0.03630.2688-0.0010.224443.138710.715813.4122
105.00352.1681-0.19217.10491.24091.5630.0201-0.3160.38990.47510.13710.1387-0.02960.173-0.21940.28270.06830.03340.2819-0.02290.226846.159517.616421.4559
112.23160.816-0.32081.6322-0.06892.31280.0476-0.1047-0.09260.1143-0.03410.2207-0.2379-0.00370.00690.1905-0.00530.02630.1505-0.00090.32640.1920.711327.4379
124.40810.1628-0.57382.84550.62196.3484-0.00910.0772-0.4669-0.1313-0.0703-0.36760.7954-0.10590.01330.26550.02520.00510.16140.02860.317146.0922-10.799932.722
133.5559-0.64791.18411.0125-0.15052.8189-0.20420.13950.3197-0.04120.0268-0.0787-0.30220.15770.13210.2204-0.0268-0.0080.21090.02540.314416.690225.88216.6535
143.15772.7499-1.53575.3401-0.88511.21370.14290.02460.2255-0.0737-0.11980.3525-0.0669-0.0268-0.03350.21520.0204-0.06040.24080.02550.24522.411120.416511.4315
151.5288-0.70920.89312.3398-1.00832.45630.10390.1018-0.1038-0.1250.00170.11190.3435-0.1023-0.05390.18180.00660.01450.2124-0.02880.21359.2777.087514.3154
164.4249-3.5504-2.37014.24072.48162.4964-0.1488-0.3042-0.20910.97030.34870.73660.0207-0.1633-0.05720.51020.01110.13260.39580.07260.3439-4.64189.164326.1356
170.8051-0.02760.99491.48730.70242.2007-0.03760.0160.08160.0081-0.0204-0.081-0.2399-0.0120.08230.1312-0.00250.01510.20080.02380.201822.583214.907427.946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 266 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 27 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 57 )
7X-RAY DIFFRACTION7chain 'B' and (resid 58 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 113 )
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 152 )
10X-RAY DIFFRACTION10chain 'B' and (resid 153 through 198 )
11X-RAY DIFFRACTION11chain 'B' and (resid 199 through 239 )
12X-RAY DIFFRACTION12chain 'B' and (resid 240 through 266 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 57 )
14X-RAY DIFFRACTION14chain 'C' and (resid 58 through 113 )
15X-RAY DIFFRACTION15chain 'C' and (resid 114 through 163 )
16X-RAY DIFFRACTION16chain 'C' and (resid 164 through 189 )
17X-RAY DIFFRACTION17chain 'C' and (resid 190 through 266 )

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