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- PDB-5g4l: Phloroglucinol reductase from Clostridium sp. with bound NADPH -

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Basic information

Entry
Database: PDB / ID: 5g4l
TitlePhloroglucinol reductase from Clostridium sp. with bound NADPH
ComponentsOXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
KeywordsOXIDOREDUCTASE / FLAVONOID DEGRADATION / ENZYME CATALYSIS / DEAROMATISATION REACTION / SHORT-CHAIN DEHYDROGENASES/REDUCTASES / NADPH DEPENDENT ENZYME
Function / homology
Function and homology information


steroid metabolic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Oxidoreductase, short chain dehydrogenase/reductase family protein
Similarity search - Component
Biological speciesCLOSTRIDIUM SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsConradt, D. / Hermann, B. / Gerhardt, S. / Einsle, O. / Mueller, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Biocatalytic Properties and Structural Analysis of Phloroglucinol Reductases.
Authors: Conradt, D. / Hermann, B. / Gerhardt, S. / Einsle, O. / Mueller, M.
History
DepositionMay 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
B: OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7274
Polymers62,2362
Non-polymers1,4912
Water10,449580
1
A: OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
B: OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
hetero molecules

A: OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
B: OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,4558
Polymers124,4734
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area22210 Å2
ΔGint-137.9 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.686, 123.083, 55.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2018-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.176971, -0.984216, -0.000345), (-0.984216, 0.176971, 0.000208), (-0.000143, 0.000377, -1)
Vector: 61.7118, 51.5847, 38.98732)

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Components

#1: Protein OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN / PHLOROGLUCINOL REDUCTASE


Mass: 31118.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U2C7W9
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL DECA-HIS EXPRESSION TAG

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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: 2.43 Å3/Da / Density % sol: 49.44 % / Description: NONE
Crystal growpH: 7.2
Details: 28 % PEG 3350 0.1 M BIS-TRIS, PH 7.2 LI2SO4 3 MM NADPH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47 Å / Num. obs: 57138 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 21.02 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G4K

5g4k


Resolution: 1.8→47.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.9473 / SU R Cruickshank DPI: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 2816 4.93 %RANDOM
Rwork0.1548 ---
obs0.1559 57079 100 %-
Displacement parametersBiso mean: 22.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.0024 Å20 Å20 Å2
2--2.4779 Å20 Å2
3----1.4754 Å2
Refine analyzeLuzzati coordinate error obs: 0.193 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3985 0 96 580 4661
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014534HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.996162HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1578SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes699HARMONIC5
X-RAY DIFFRACTIONt_it4534HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion16.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion586SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6039SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2391 211 5.07 %
Rwork0.2026 3951 -
all0.2045 4162 -
obs--100 %
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)
10.4832-0.0442-0.00280.6215-0.01280.10410.00660.04940.1481-0.1363-0.016-0.0143-0.00510.00060.0094-0.00320.0019-0.0051-0.03420.0086-0.0405-0.463620.518514.153
20.5424-0.1355-0.00670.58610.01060.0402-0.0133-0.0418-0.0138-0.0186-0.00410.17580.0036-0.00220.0174-0.03080.0022-0.0123-0.0217-0.0071-0.026-20.38012.803124.6132

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