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- PDB-5krq: Renalase in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 5krq
TitleRenalase in complex with NADPH
ComponentsRenalase
KeywordsOXIDOREDUCTASE / Renalase / substrate binding / NADPH
Function / homology
Function and homology information


renalase / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / FAD binding / NAD binding / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Bacterial renalase / NAD(P)-binding Rossmann-like domain / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Bacterial renalase / NAD(P)-binding Rossmann-like domain / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-NDP / Renalase / Renalase
Similarity search - Component
Biological speciesPseudomonas savastanoi pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.086 Å
AuthorsSilvaggi, N.R. / Moran, G.R. / Roman, J.V.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1402475 United States
National Science Foundation (NSF, United States)CHE-1403293 United States
National Science Foundation (NSF, United States)MCB-1157392 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K02 AI093675 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2016
Title: Ligand binding phenomena that pertain to the metabolic function of renalase.
Authors: Beaupre, B.A. / Roman, J.V. / Hoag, M.R. / Meneely, K.M. / Silvaggi, N.R. / Lamb, A.L. / Moran, G.R.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Renalase
B: Renalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7716
Polymers73,7092
Non-polymers3,0624
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.445, 71.046, 74.807
Angle α, β, γ (deg.)90.00, 107.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Renalase


Mass: 36854.434 Da / Num. of mol.: 2 / Mutation: G145S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria)
Gene: ALO55_03823 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P9WWR6, UniProt: Q48MT7*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2 M sodium formate, 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2015
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.086→46.02 Å / Num. obs: 37538 / % possible obs: 98 % / Redundancy: 3.2 % / Biso Wilson estimate: 24.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.21
Reflection shellResolution: 2.086→2.161 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.57 / CC1/2: 0.888 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
HKL-2000712data reduction
SCALEPACK712data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKJ

3kkj


Resolution: 2.086→46.02 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1860 5 %Random selection
Rwork0.1568 ---
obs0.1591 37198 98.26 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å
Displacement parametersBiso mean: 35.39 Å2
Refinement stepCycle: LAST / Resolution: 2.086→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4922 0 172 279 5373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115243
X-RAY DIFFRACTIONf_angle_d1.2257169
X-RAY DIFFRACTIONf_dihedral_angle_d13.7313003
X-RAY DIFFRACTIONf_chiral_restr0.057758
X-RAY DIFFRACTIONf_plane_restr0.007905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0861-2.16070.28711600.1963037X-RAY DIFFRACTION85
2.1607-2.24720.22861850.17993499X-RAY DIFFRACTION98
2.2472-2.34940.23971880.16783590X-RAY DIFFRACTION100
2.3494-2.47330.23481880.16763564X-RAY DIFFRACTION100
2.4733-2.62820.24471880.16893587X-RAY DIFFRACTION100
2.6282-2.83110.23971890.17633581X-RAY DIFFRACTION100
2.8311-3.1160.21921890.17263578X-RAY DIFFRACTION100
3.116-3.56670.18321900.1523626X-RAY DIFFRACTION100
3.5667-4.49310.16681900.12513608X-RAY DIFFRACTION100
4.4931-46.03380.17021930.14923668X-RAY DIFFRACTION100
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)
12.57530.0318-1.30511.1239-0.15595.0869-0.0099-0.04850.14160.01640.0344-0.0404-0.10560.23-0.03640.1303-0.0136-0.04620.13130.0040.18499.70438.0455-4.9809
22.2974-0.514-1.67881.3851-0.2253.9527-0.165-0.3876-0.31950.06910.10730.09870.25520.5480.06640.21920.037-0.04120.29390.04690.22648.84993.402612.0355
33.55881.54722.38785.51353.1416.3767-0.12540.34480.0357-0.50460.0502-0.0201-0.47710.1484-0.03310.1695-0.0466-0.01650.2040.0910.14996.894711.0523-20.5556
40.4746-0.3416-0.47250.63340.83063.2782-0.0613-0.0408-0.00750.022-0.06480.0246-0.110.07720.11520.1130.0041-0.02010.13360.03860.1687-1.4098.28922.8033
54.8042-1.40951.66775.33692.00196.15860.03680.0609-0.4008-0.0698-0.18180.183-0.2611-0.24170.14180.1331-0.04280.03190.20190.020.174-15.177310.53259.1573
61.0163-0.5019-0.95591.03851.62062.5676-0.1675-0.1483-0.15760.19590.00070.22980.22950.06690.13460.22940.0250.01580.21380.05780.1753-5.32627.61666.3091
74.05490.558-0.65693.2610.1665.5497-0.0520.1416-0.22570.01290.0214-0.28740.27760.2250.08860.15330.0485-0.00690.13650.00360.21510.0122-3.4353-11.2257
81.5062-0.0609-1.05680.51680.29363.54170.05610.38470.124-0.10520.03960.1021-0.1695-0.4358-0.06180.19790.0546-0.02620.27850.05560.2653-21.624410.8317-38.1076
94.2243-0.70220.7936.4323-1.81386.30480.0961-0.51460.23580.45080.0018-0.006-0.19140.1046-0.16670.18340.01450.02880.2014-0.08960.1681-18.790613.5698-12.9069
101.71940.2785-1.26270.4539-0.41552.6190.05970.13760.1999-0.0510.030.0432-0.1878-0.0641-0.03830.15120.02-0.02060.16130.01380.1883-6.97669.9846-37.4786
113.47850.788-2.81161.2658-0.88774.3228-0.08510.114-0.1256-0.04290.00450.0640.1773-0.06730.11030.15580.01-0.05370.15240.00990.206-17.60774.1596-29.951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 142 )
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 233 )
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 260 )
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 289 )
7X-RAY DIFFRACTION7chain 'A' and (resid 290 through 328 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 117 )
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 142 )
10X-RAY DIFFRACTION10chain 'B' and (resid 143 through 260 )
11X-RAY DIFFRACTION11chain 'B' and (resid 261 through 330 )

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