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- PDB-7s5f: Crystal structure of mannose-6-phosphate reductase from celery (A... -

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Basic information

Entry
Database: PDB / ID: 7s5f
TitleCrystal structure of mannose-6-phosphate reductase from celery (Apium graveolens) leaves with NADP+ and mannonic acid bound
ComponentsManose-6-phosphate reductase
KeywordsOXIDOREDUCTASE / aldo/keto reductase superfamily / aldose-6-phosphate reductase / Apium graveolens / celery / mannose-6-phosphate reductase / peach / Prunus persica
Function / homology
Function and homology information


aldose-6-phosphate reductase (NADPH) activity / D-threo-aldose 1-dehydrogenase activity
Similarity search - Function
Aldo-keto reductase family 2A / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
D-MANNONIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Manose-6-phosphate reductase
Similarity search - Component
Biological speciesApium graveolens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsZheng, Y. / Bhayani, J.A. / Romina, I.M. / Hartman, M.D. / Cereijo, A.E. / Ballicora, M.A. / Iglesias, A.A. / Figueroa, C.M. / Liu, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1616851 United States
CitationJournal: Plant Cell.Physiol. / Year: 2022
Title: Structural Determinants of Sugar Alcohol Biosynthesis in Plants: The Crystal Structures of Mannose-6-Phosphate and Aldose-6-Phosphate Reductases.
Authors: Minen, R.I. / Bhayani, J.A. / Hartman, M.D. / Cereijo, A.E. / Zheng, Y. / Ballicora, M.A. / Iglesias, A.A. / Liu, D. / Figueroa, C.M.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Manose-6-phosphate reductase
A: Manose-6-phosphate reductase
C: Manose-6-phosphate reductase
D: Manose-6-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,68012
Polymers140,9224
Non-polymers3,7588
Water30,0491668
1
B: Manose-6-phosphate reductase
hetero molecules

D: Manose-6-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3406
Polymers70,4612
Non-polymers1,8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area6620 Å2
ΔGint-25 kcal/mol
Surface area23360 Å2
MethodPISA
2
A: Manose-6-phosphate reductase
C: Manose-6-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3406
Polymers70,4612
Non-polymers1,8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-25 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.202, 61.779, 148.063
Angle α, β, γ (deg.)90.000, 107.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-594-

HOH

21B-936-

HOH

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Components

#1: Protein
Manose-6-phosphate reductase


Mass: 35230.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apium graveolens (plant) / Gene: M6PR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9WT24
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CS2 / D-MANNONIC ACID / D-MANNONATE


Mass: 196.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1668 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 0.2 M ammonium formate, 20% (w/v) PEG 3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 132086 / % possible obs: 95.8 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15
Reflection shellResolution: 1.72→1.76 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6719 / CC1/2: 0.71

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2iki

2iki


Resolution: 1.72→38.07 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 6461 5.01 %
Rwork0.1808 122574 -
obs0.1823 129035 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.02 Å2 / Biso mean: 25.9943 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 1.72→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9835 0 244 1668 11747
Biso mean--21.78 33.73 -
Num. residues----1236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510367
X-RAY DIFFRACTIONf_angle_d0.9614060
X-RAY DIFFRACTIONf_dihedral_angle_d22.0011463
X-RAY DIFFRACTIONf_chiral_restr0.071596
X-RAY DIFFRACTIONf_plane_restr0.0061748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.740.31471390.2583044318369
1.74-1.760.29512220.24183699392185
1.76-1.790.27362130.22633881409490
1.79-1.810.24682210.21934044426593
1.81-1.830.26182130.21194092430595
1.83-1.860.24712150.2094173438896
1.86-1.880.26292130.20924227444097
1.88-1.910.22722270.19744214444197
1.91-1.940.23972320.20124224445697
1.94-1.970.24312120.19224249446198
1.97-2.010.21922340.19064243447797
2.01-2.040.22951940.18914262445697
2.04-2.080.23851940.19064269446397
2.08-2.130.24122480.19634243449198
2.13-2.170.21882280.18334271449998
2.17-2.220.19132510.17844248449998
2.22-2.280.21472340.18374257449198
2.28-2.340.21232140.1824229444397
2.34-2.410.23232040.17834229443397
2.41-2.490.20282160.17364208442496
2.49-2.580.20162100.17174211442196
2.58-2.680.20432110.17624143435495
2.68-2.80.21382240.18064132435695
2.8-2.950.2062120.17664057426993
2.95-3.130.19491900.17534005419591
3.13-3.380.19622270.1694057428492
3.38-3.710.182440.15744139438394
3.71-4.250.18092330.15383902413589
4.25-5.350.17551970.15853698389583
5.35-38.070.24331890.21013924411386
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)
14.4463-0.44851.62612.99911.012.7740.06120.1636-0.2581-0.19940.1292-0.38510.04280.2736-0.17330.18030.04240.0280.1537-0.02190.0743-19.782244.619840.9627
21.687-0.5002-0.18331.47980.46381.21950.1960.31130.1049-0.2818-0.0666-0.28070.10380.1729-0.11420.16810.0610.04060.21620.0130.1493-18.822851.887533.794
31.8906-0.04330.16672.07840.3751.72240.08180.21730.1474-0.1427-0.1001-0.05190.05040.07380.02970.11730.03980.02150.13510.03990.1047-32.088759.879938.2573
43.07810.03411.0871.22580.10661.11830.037-0.0147-0.09510.1280.0192-0.09120.01310.0437-0.0590.13310.00570.00560.0890.00750.0715-28.259849.266851.9528
51.5274-0.3725-0.12052.0175-1.1062.58750.0458-0.0157-0.130.1921-0.0684-0.30230.11380.18490.01010.17360.0233-0.04920.1049-0.0090.1884-16.40738.08655.8554
61.1060.6639-1.98093.0165-0.26754.5091-0.1121-0.064-0.2382-0.0206-0.0235-0.14320.45320.19810.18580.18420.0644-0.08260.15990.02490.2157-16.44435.366355.8473
71.86380.2565-0.27086.0289-2.75152.6889-0.0391-0.02920.22690.28120.0401-0.0352-0.08130.05730.00510.14850.0022-0.00090.1499-0.01820.17-24.42459.982656.6036
83.31-0.05641.15633.7149-1.23742.44810.0875-0.4986-0.17540.2378-0.04260.33250.2284-0.5472-0.00010.2844-0.1376-0.02080.3557-0.02540.0725-1.572614.285629.9747
90.38880.3285-0.34410.2838-0.29630.31190.1415-0.36770.14270.2694-0.08930.31950.1503-0.448-0.12330.2537-0.28310.11390.7553-0.04890.2056-8.962216.384436.9291
101.30040.205-0.25140.0554-0.1450.70610.2063-0.58220.24970.2865-0.2180.17670.1546-0.4384-0.09640.259-0.18280.04540.4833-0.07130.1292.405723.773238.597
111.9460.0186-0.06180.837-0.12421.77540.1494-0.41270.23470.2553-0.2465-0.09420.0141-0.15210.08330.162-0.0929-0.00980.2466-0.05140.144911.292228.995633.7742
122.56620.7180.68861.45240.11010.89240.0852-0.0040.0012-0.1538-0.08090.09990.165-0.1601-0.01190.1758-0.02180.00720.1616-0.01060.07451.930116.572117.6208
132.0393-0.1213-1.13013.3861-0.063.83480.02090.0489-0.2929-0.1126-0.08360.17090.4301-0.42690.06630.1974-0.0923-0.06320.2828-0.02780.1481-5.90567.283714.351
143.56691.16370.90085.44461.83863.5772-0.04650.10190.591-0.3708-0.02430.1317-0.0232-0.16350.06250.15390.0032-0.00540.15010.00360.23052.491931.565516.2592
151.84091.1470.02071.162-0.95492.1201-0.22390.30580.0276-0.3495-0.1515-0.56370.08650.49680.28540.32880.03880.11360.34950.20730.479131.670646.06023.5179
160.65040.04170.46760.6351-0.05240.4989-0.21390.32690.0321-0.3074-0.2712-0.72710.06850.62690.09850.11720.11520.32780.46030.34020.69637.048938.146810.0015
171.9410.39880.21660.64111.48723.76580.07490.1954-0.4580.06070.0319-0.41420.73680.3688-0.08220.43590.13010.1720.2390.07050.460626.74217.574314.8256
181.22120.2001-0.35150.26690.19970.5968-0.0654-0.05040.09610.0337-0.3067-0.31580.00940.27440.27170.1557-0.0024-0.02310.19950.16480.300326.31838.141622.7115
192.35630.69260.56950.619-0.96714.6717-0.16850.19410.0772-0.24810.0609-0.03380.3466-0.03320.09710.25180.02270.00980.10230.02890.207415.459540.9818.6908
202.51450.07730.10433.0412-0.71722.8362-0.10680.31540.0722-0.5602-0.00370.06150.1667-0.15410.10540.28090.0146-0.01110.17810.03990.175715.157347.7435-2.1695
214.7008-0.1199-0.09673.2235-0.31191.2996-0.00780.4640.5584-0.4098-0.0646-0.0962-0.1188-0.1150.03180.3140.0367-0.05230.25810.10510.199115.31352.6412-1.7392
223.4729-2.12350.32424.0238-0.30592.2165-0.24110.0027-0.0979-0.10690.10420.38460.43370.08220.12910.3354-0.03370.08620.1730.01580.238814.825128.33136.8088
232.0024-0.4396-0.14152.9825-0.50195.4814-0-0.13640.08530.30870.08190.2818-0.2557-0.1692-0.12160.04240.03330.00680.1265-0.00920.151924.559442.606766.1499
241.4001-0.5976-0.50832.15521.09681.8554-0.088-0.02240.06920.10.04090.18230.005-0.16280.06070.0760.0013-0.00140.12890.01140.109716.905736.553763.1937
251.299-0.6535-0.11392.6651-0.1211.32080.00330.0788-0.0286-0.1076-0.01320.10830.0419-0.07230.00540.0876-0.0249-0.00420.1293-0.01160.087325.168129.438751.1205
260.6850.05780.32561.05280.56141.9868-0.0024-0.03420.00220.13910.0494-0.1237-0.03510.0429-0.0440.09370.0032-0.02110.0632-0.00510.114137.471340.32966.4939
275.00090.1106-0.69193.31330.37920.98060.052-0.30230.39520.21030.0059-0.0384-0.07830.0816-0.05820.17810.0094-0.05420.1221-0.03210.080437.920748.529676.0862
283.57982.34841.08484.88651.82272.4258-0.02320.0224-0.15610.23650.0422-0.18390.2492-0.0193-0.0350.1370.0214-0.00370.11380.00730.130138.874325.214364.8622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 25 )B1 - 25
2X-RAY DIFFRACTION2chain 'B' and (resid 26 through 121 )B26 - 121
3X-RAY DIFFRACTION3chain 'B' and (resid 122 through 163 )B122 - 163
4X-RAY DIFFRACTION4chain 'B' and (resid 164 through 229 )B164 - 229
5X-RAY DIFFRACTION5chain 'B' and (resid 230 through 264 )B230 - 264
6X-RAY DIFFRACTION6chain 'B' and (resid 265 through 290 )B265 - 290
7X-RAY DIFFRACTION7chain 'B' and (resid 291 through 309 )B291 - 309
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 25 )A1 - 25
9X-RAY DIFFRACTION9chain 'A' and (resid 26 through 62 )A26 - 62
10X-RAY DIFFRACTION10chain 'A' and (resid 63 through 121 )A63 - 121
11X-RAY DIFFRACTION11chain 'A' and (resid 122 through 163 )A122 - 163
12X-RAY DIFFRACTION12chain 'A' and (resid 164 through 264 )A164 - 264
13X-RAY DIFFRACTION13chain 'A' and (resid 265 through 290 )A265 - 290
14X-RAY DIFFRACTION14chain 'A' and (resid 291 through 309 )A291 - 309
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 36 )C1 - 36
16X-RAY DIFFRACTION16chain 'C' and (resid 37 through 121 )C37 - 121
17X-RAY DIFFRACTION17chain 'C' and (resid 122 through 137 )C122 - 137
18X-RAY DIFFRACTION18chain 'C' and (resid 138 through 184 )C138 - 184
19X-RAY DIFFRACTION19chain 'C' and (resid 185 through 220 )C185 - 220
20X-RAY DIFFRACTION20chain 'C' and (resid 221 through 264 )C221 - 264
21X-RAY DIFFRACTION21chain 'C' and (resid 265 through 290 )C265 - 290
22X-RAY DIFFRACTION22chain 'C' and (resid 291 through 309 )C291 - 309
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 25 )D1 - 25
24X-RAY DIFFRACTION24chain 'D' and (resid 26 through 121 )D26 - 121
25X-RAY DIFFRACTION25chain 'D' and (resid 122 through 163 )D122 - 163
26X-RAY DIFFRACTION26chain 'D' and (resid 164 through 264 )D164 - 264
27X-RAY DIFFRACTION27chain 'D' and (resid 265 through 290 )D265 - 290
28X-RAY DIFFRACTION28chain 'D' and (resid 291 through 309 )D291 - 309

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