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- PDB-4q3m: Crystal structure of MGS-M4, an aldo-keto reductase enzyme from a... -

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Basic information

Entry
Database: PDB / ID: 4q3m
TitleCrystal structure of MGS-M4, an aldo-keto reductase enzyme from a Medee basin deep-sea metagenome library
ComponentsMGS-M4
KeywordsHYDROLASE / metagenome / metagenomic library / OXIDOREDUCTASE / ALPHA/BETA BARREL / TIM BARREL / UNKNOWN SUBSTRATE
Function / homology
Function and homology information


small molecule metabolic process / :
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / 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 / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsStogios, P.J. / Xu, X. / Cui, H. / Alcaide, M. / Ferrer, M. / Savchenko, A.
CitationJournal: Environ Microbiol / Year: 2015
Title: Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.
Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / ...Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / Jebbar, M. / Jaeger, K.E. / Yakimov, M.M. / Yakunin, A.F. / Golyshin, P.N. / Golyshina, O.V. / Savchenko, A. / Ferrer, M.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: MGS-M4
B: MGS-M4
C: MGS-M4
D: MGS-M4
E: MGS-M4
F: MGS-M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,60513
Polymers191,0066
Non-polymers5997
Water14,088782
1
A: MGS-M4
B: MGS-M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8614
Polymers63,6692
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-44 kcal/mol
Surface area22270 Å2
MethodPISA
2
C: MGS-M4
D: MGS-M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8614
Polymers63,6692
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-47 kcal/mol
Surface area22300 Å2
MethodPISA
3
E: MGS-M4
F: MGS-M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8845
Polymers63,6692
Non-polymers2153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-44 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.469, 172.469, 113.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein
MGS-M4


Mass: 31834.264 Da / Num. of mol.: 6 / Fragment: MGS-M4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Gene: MGS-M4 / Plasmid: p15-TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A0A0B5KNF6*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / Source method: isolated from a natural source / Formula: H2O
Source detailsTHE SAMPLE WAS EXTRACTED FROM MEDEE BASIN DEEP-SEA AND ANALYZED BY USING METAGENOME LIBRARY TECHNIQUE

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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: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M ammonium sulphate, 25% PEG3350, TEV protease in 1/20 molar ratio protein:TEV, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 10, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→25 Å / Num. obs: 59489 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 19.05
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 3.01 / % possible all: 99.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: dev_1538)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FZI

4fzi


Resolution: 2.552→24.579 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 29.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1989 3.35 %
Rwork0.2067 --
obs0.2087 59408 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.552→24.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13330 0 31 782 14143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413650
X-RAY DIFFRACTIONf_angle_d0.74518467
X-RAY DIFFRACTIONf_dihedral_angle_d13.3575073
X-RAY DIFFRACTIONf_chiral_restr0.0352032
X-RAY DIFFRACTIONf_plane_restr0.0042362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5517-2.61540.31081440.2714198X-RAY DIFFRACTION98
2.6154-2.68610.30261430.27754273X-RAY DIFFRACTION100
2.6861-2.7650.34041450.25894258X-RAY DIFFRACTION100
2.765-2.85410.33211490.25254241X-RAY DIFFRACTION100
2.8541-2.9560.33671480.24454263X-RAY DIFFRACTION99
2.956-3.07410.3341450.25194243X-RAY DIFFRACTION99
3.0741-3.21370.27131470.23864156X-RAY DIFFRACTION98
3.2137-3.38280.33991440.23374168X-RAY DIFFRACTION97
3.3828-3.59410.28681390.21334020X-RAY DIFFRACTION94
3.5941-3.87060.25241360.19773923X-RAY DIFFRACTION92
3.8706-4.25830.20751360.1713887X-RAY DIFFRACTION91
4.2583-4.87030.2231330.15153879X-RAY DIFFRACTION90
4.8703-6.12040.21371430.17933998X-RAY DIFFRACTION93
6.1204-24.58040.23391370.18533912X-RAY DIFFRACTION89
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)
13.9137-4.4762-3.64115.91332.02569.0307-0.40690.13860.0922-0.91820.6083-0.26980.70790.2566-0.19330.5925-0.12380.03710.39450.00750.488517.547870.9344-51.057
23.79660.6309-0.3467.5960.16852.0691-0.1420.534-0.4856-1.22790.2793-0.49220.10760.0432-0.10270.6528-0.1060.06010.4713-0.04070.324518.901375.3489-56.5632
32.33420.38630.42944.28220.02351.4499-0.0503-0.0025-0.3111-0.27830.24870.00710.0304-0.1192-0.19680.2506-0.04860.02240.33640.04670.304816.677877.9971-41.8981
42.15170.56990.69418.2576-0.9872.11750.0326-0.1247-0.7546-0.50670.226-0.06840.2956-0.1881-0.24610.27070.0128-0.03370.34780.0420.56222.320568.6261-37.2746
56.0826-4.31462.27735.6143-1.66773.13290.0528-0.6403-0.17130.1701-0.10110.1578-0.2585-0.34570.07120.59030.0261-0.08550.6435-0.15290.46635.290898.0936-12.49
64.32822.11950.04634.3303-0.7532.14010.6756-1.6214-0.09130.799-0.7237-0.5767-0.1514-0.1540.01180.5738-0.0696-0.10830.9699-0.01260.431233.503393.241-6.3479
73.54870.72470.52052.2525-0.06852.88940.1342-0.85210.15880.2957-0.0329-0.1276-0.4021-0.4787-0.10540.33840.0539-0.02620.4975-0.08180.399328.263894.8234-20.3447
84.28162.34610.32085.5521-0.16052.53560.1566-0.42340.29620.2003-0.0844-0.2041-0.32040.1536-0.09480.30520.02070.02280.3636-0.09620.474638.541995.054-26.259
95.91341.89551.04363.54184.85397.1907-0.04610.875-0.32280.07760.2696-0.16450.5236-0.3705-0.17450.4336-0.021-0.00340.61440.07220.3186-16.232770.2919-13.4543
105.97411.94810.59024.2626-0.06881.8528-0.21431.5221-0.4842-0.55960.30150.24720.35-0.2649-0.06960.4627-0.0135-0.03270.8056-0.05720.3274-11.496571.3042-18.9931
113.3880.4883-0.3033.077-0.75781.64250.02410.4233-0.173-0.00310.1690.1549-0.0518-0.1728-0.18920.23280.07370.00870.3168-0.00430.2869-10.495274.4091-4.3315
128.90683.53231.06863.9286-0.99752.29580.01830.1487-0.76190.00930.31890.25710.0625-0.2936-0.34240.35620.08350.01520.27640.02230.4476-15.755464.76150.1412
133.48440.1356-0.76447.015-0.03642.5002-0.1125-0.6731-0.1210.834-0.2343-0.4584-0.20060.82440.23650.73170.0406-0.27040.69-0.04380.419815.452567.017325.6279
144.4637-0.74710.19272.588-0.5531.3664-0.333-1.2878-0.39830.88520.4285-0.2717-0.12380.0515-0.10170.89810.2195-0.17410.73190.02650.443811.006767.01831.16
152.5563-0.53690.15452.086-0.5372.6961-0.1359-0.41230.09620.66020.1472-0.3352-0.3380.1548-0.01710.4922-0.001-0.1430.324-0.01280.39429.811572.584117.3268
166.7173-1.2358-0.15491.9648-0.29692.381-0.0105-0.2714-0.34270.252-0.0146-0.42920.20350.41940.02680.45750.0361-0.10070.3415-0.01340.461815.164963.832811.314
174.5766-1.7417-0.2122.19132.84185.14750.0672-0.82650.37920.20180.0829-0.0695-0.2118-0.4055-0.18970.3917-0.00480.06630.52550.03410.3033-15.871829.58122.4515
184.5305-0.13840.26982.5082-0.29191.14990.1033-1.43530.57420.3590.07660.2994-0.1675-0.1549-0.12570.363-0.02690.05280.6561-0.06540.2966-11.604528.326327.9599
193.6674-0.57320.4743.0067-0.84921.91220.0274-0.32990.03520.08030.14410.34320.0347-0.2355-0.15870.2209-0.05330.00630.2608-0.00610.2536-10.457225.169213.2848
206.8332-1.894-0.14112.4259-0.62952.1117-0.0463-0.37530.5176-0.16520.27550.318-0.2028-0.3202-0.21170.3644-0.0461-0.01240.2510.03890.4535-15.738634.80958.7073
216.45322.91130.14715.48181.3233.6554-0.61850.77360.4917-0.87680.1816-1.10230.35080.3290.31220.5778-0.13240.24610.5528-0.04520.361915.623732.5815-16.5606
224.22830.28680.27681.98170.1461.5695-0.2460.6590.4485-0.63410.3932-0.185-0.0371-0.0525-0.14020.7142-0.16310.11470.61080.10740.39939.780332.7557-21.631
233.50240.91-0.1072.2566-0.47952.6482-0.18580.4104-0.0304-0.57630.2348-0.17880.46120.1735-0.05430.47290.00990.09610.2396-0.00020.30149.851926.9668-8.3345
244.16221.5088-0.15783.2993-0.07742.9436-0.07480.17730.4972-0.44590.0961-0.35030.10540.5002-0.01040.3173-0.01150.08840.2753-0.01460.383215.12535.8158-2.39
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:29 )A2 - 29
2X-RAY DIFFRACTION2( CHAIN A AND RESID 30:85 )A30 - 85
3X-RAY DIFFRACTION3( CHAIN A AND RESID 86:223 )A86 - 223
4X-RAY DIFFRACTION4( CHAIN A AND RESID 224:274 )A224 - 274
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:29 )B2 - 29
6X-RAY DIFFRACTION6( CHAIN B AND RESID 30:85 )B30 - 85
7X-RAY DIFFRACTION7( CHAIN B AND RESID 86:223 )B86 - 223
8X-RAY DIFFRACTION8( CHAIN B AND RESID 224:274 )B224 - 274
9X-RAY DIFFRACTION9( CHAIN C AND RESID 2:29 )C2 - 29
10X-RAY DIFFRACTION10( CHAIN C AND RESID 30:85 )C30 - 85
11X-RAY DIFFRACTION11( CHAIN C AND RESID 86:223 )C86 - 223
12X-RAY DIFFRACTION12( CHAIN C AND RESID 224:274 )C224 - 274
13X-RAY DIFFRACTION13( CHAIN D AND RESID 2:29 )D2 - 29
14X-RAY DIFFRACTION14( CHAIN D AND RESID 30:85 )D30 - 85
15X-RAY DIFFRACTION15( CHAIN D AND RESID 86:223 )D86 - 223
16X-RAY DIFFRACTION16( CHAIN D AND RESID 224:274 )D224 - 274
17X-RAY DIFFRACTION17( CHAIN E AND RESID 3:29 )E3 - 29
18X-RAY DIFFRACTION18( CHAIN E AND RESID 30:85 )E30 - 85
19X-RAY DIFFRACTION19( CHAIN E AND RESID 86:223 )E86 - 223
20X-RAY DIFFRACTION20( CHAIN E AND RESID 224:274 )E224 - 274
21X-RAY DIFFRACTION21( CHAIN F AND RESID 2:29 )F2 - 29
22X-RAY DIFFRACTION22( CHAIN F AND RESID 30:85 )F30 - 85
23X-RAY DIFFRACTION23( CHAIN F AND RESID 86:223 )F86 - 223
24X-RAY DIFFRACTION24( CHAIN F AND RESID 224:274 )F224 - 274

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