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- PDB-4zcc: Renalase in complex with NADH -

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Basic information

Entry
Database: PDB / ID: 4zcc
TitleRenalase in complex with NADH
ComponentsRenalase
KeywordsOXIDOREDUCTASE / Renalase / oxidase / flavoenzyme
Function / homology
Function and homology information


renalase / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / FAD binding / NAD binding / NADP 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 / FORMIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Renalase
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsSilvaggi, N.R. / Moran, G.R. / Roman, J.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1402475 United States
National Science Foundation (NSF, United States)MCB-1157392 United States
CitationJournal: Biochemistry / Year: 2015
Title: Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-beta-NAD(P) Oxidase Activity from Pseudomonas phaseolicola.
Authors: Hoag, M.R. / Roman, J. / Beaupre, B.A. / Silvaggi, N.R. / Moran, G.R.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _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 1.3Sep 27, 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
C: Renalase
D: Renalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,40616
Polymers147,4184
Non-polymers5,98812
Water13,259736
1
A: Renalase
D: Renalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7038
Polymers73,7092
Non-polymers2,9946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renalase
C: Renalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7038
Polymers73,7092
Non-polymers2,9946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.500, 71.500, 143.800
Angle α, β, γ (deg.)90.00, 97.50, 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.: 4 / Mutation: G145S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6) (bacteria)
Strain: 1448A / Race 6 / Gene: PSPPH_1014 / Variant: Race 6 / Plasmid: pET21-NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48MT7, renalase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 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: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.997→46.224 Å / Num. obs: 86594 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.7
Reflection shellResolution: 1.997→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1965refinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKJ

3kkj


Resolution: 1.997→46.224 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2892 3.59 %Random selection
Rwork0.1697 ---
obs0.1713 80613 92.81 %-
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.997→46.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 400 736 11042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410620
X-RAY DIFFRACTIONf_angle_d1.63414522
X-RAY DIFFRACTIONf_dihedral_angle_d17.9673754
X-RAY DIFFRACTIONf_chiral_restr0.0721541
X-RAY DIFFRACTIONf_plane_restr0.0091836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.997-2.06840.26492200.21445882X-RAY DIFFRACTION71
2.0684-2.15120.2682640.20436951X-RAY DIFFRACTION83
2.1512-2.24910.24642870.1937703X-RAY DIFFRACTION93
2.2491-2.36770.22892970.18227926X-RAY DIFFRACTION95
2.3677-2.5160.23772990.17448048X-RAY DIFFRACTION96
2.516-2.71020.22083020.17398075X-RAY DIFFRACTION97
2.7102-2.98290.2313010.17758223X-RAY DIFFRACTION98
2.9829-3.41440.22753050.17258266X-RAY DIFFRACTION99
3.4144-4.30140.18563070.14758296X-RAY DIFFRACTION99
4.3014-46.23630.18093100.1578351X-RAY DIFFRACTION97
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)
11.3785-0.1460.72720.4644-0.13872.4963-0.0714-0.1294-0.07410.07610.06240.05170.0912-0.1632-0.04910.18270.00010.04160.1352-0.02490.1815-0.1762-8.6641-75.8637
22.674-0.35211.86710.5414-0.34643.5533-0.1599-0.55030.26610.0770.1742-0.2217-0.3217-0.6802-0.02590.23210.08010.00340.2613-0.08070.2457-1.5163-2.7253-59.111
30.8562-0.28250.15120.3501-0.28681.7992-0.0441-0.0160.0450.00840.0734-0.02530.1007-0.065-0.03950.2011-0.01110.03070.1233-0.03970.22562.7414-8.6179-74.5922
40.4766-0.28140.15050.4091-0.68711.6846-0.0203-0.02910.0190.07220.0009-0.0280.0280.00030.02450.2035-0.00940.00450.1328-0.04010.183310.8168-8.9875-68.1402
52.8484-0.6026-1.80362.7878-0.58057.783-0.0412-0.03180.22410.13790.054-0.19370.23380.5518-0.02840.1196-0.021-0.03740.166-0.03240.164524.5702-11.249-61.7466
60.3774-0.4670.50770.7136-1.01761.7199-0.1662-0.08320.10250.25350.039-0.1918-0.1298-0.01030.10730.2710.0367-0.0220.1759-0.04980.172314.732-8.2529-64.7512
72.50020.21410.1581.75490.224.2745-0.04080.12960.28270.09690.0380.1197-0.3363-0.07960.06040.16870.029-0.00260.08260.0010.1715-0.47612.8688-82.1974
81.5624-0.05890.81190.6876-0.14072.9959-0.0374-0.1074-0.04780.02410.0455-0.00780.0705-0.1449-0.06380.1582-0.00620.01450.11790.02130.1601-22.5247-10.092-147.1161
93.8576-0.53751.79441.1875-0.15373.4502-0.1124-0.50850.22270.11560.1357-0.1012-0.3124-0.6396-0.00730.20450.05260.02050.2732-0.0360.2036-24.0062-4.3826-130.3768
101.0806-0.21170.0260.56690.09012.2132-0.0579-0.0597-0.03360.04270.0348-0.02010.1518-0.12990.0480.16290.00350.02360.1342-0.0070.212-19.6412-9.9751-145.8242
110.8028-0.32250.46070.4687-0.41842.0477-0.0058-0.01950.08260.0128-0.0417-0.01990.10890.05370.04320.17220.00540.00620.1212-0.03060.1906-10.8512-8.9601-142.1173
121.8555-1.72130.72631.7943-0.27481.10860.1134-0.1026-0.24910.0564-0.0010.40370.147-0.2003-0.09590.158-0.0108-0.01190.2312-0.01020.2381-15.0839-16.9639-126.3268
132.7559-0.2871-2.31962.7179-1.39637.3001-0.1643-0.01390.1456-0.0121-0.0673-0.14170.01760.43150.2070.1186-0.0148-0.03980.14210.00610.18942.2131-12.7129-132.8286
140.3906-0.39160.53920.4936-0.63281.0773-0.1165-0.13360.10510.29260.0489-0.0477-0.2271-0.10060.08080.29590.0362-0.00760.1693-0.02640.1928-7.7166-9.7333-135.9256
152.31990.2221-0.32631.56090.07822.55970.02030.05090.1903-0.06280.03310.0624-0.2098-0.1085-0.02350.16780.0193-0.00770.1110.00620.173-22.45891.4516-153.0223
160.7680.15471.26730.486-0.31852.8770.11190.2625-0.1663-0.0575-0.0222-0.00240.16310.3293-0.09970.1750.06160.0090.2528-0.05070.1899.6598-12.7384-177.491
171.03510.00150.20650.4253-0.24872.56210.0280.0638-0.14870.05880.0741-0.00160.08490.1682-0.07830.16790.02120.00550.141-0.0110.22186.4434-13.1965-172.0419
180.9229-0.01850.77610.33050.04582.18110.05220.0889-0.1684-0.0644-0.0172-0.05990.11820.0394-0.01530.150.00960.02790.1362-0.00630.2275-2.0514-10.4172-175.9043
193.2654-0.0295-1.1122.01120.54183.9807-0.0755-0.2203-0.17-0.01190.0735-0.17360.326-0.17860.00810.165-0.025-0.00530.2094-0.03450.189-11.9845-13.0863-186.7354
201.6913-0.0081.22120.4457-0.09881.2336-0.0280.1713-0.02010.0206-0.0194-0.0844-0.07050.07570.0750.16970.00320.02360.20130.01870.17225.2061-5.5366-171.7549
213.05860.72160.2391.32820.37681.19730.08220.0426-0.24250.07280.0895-0.18480.04910.1942-0.17540.15370.0485-0.01230.2139-0.05390.183236.6304-12.8369-92.0469
221.3712-0.27880.84440.52440.82593.09040.1420.1844-0.2456-0.051-0.04580.23730.285-0.0936-0.02330.17920.0193-0.04130.1827-0.05380.267524.9362-16.6437-107.7055
234.81120.39452.82380.22950.01943.42730.01030.79110.0837-0.04320.0844-0.0626-0.12410.7201-0.07610.17750.00420.01410.3419-0.04240.217633.8924-10.5965-116.8408
240.87310.14350.11450.30440.1732.88140.11370.1115-0.02860.02560.0836-0.10460.1060.0873-0.15940.13360.02840.00860.1347-0.01410.224628.7294-13.1024-100.6189
251.41060.03940.58780.1040.43441.64340.08650.1451-0.1880.0059-0.0155-0.04740.0916-0.0116-0.03470.1759-0.00170.00030.1222-0.01670.227620.4785-12.5604-107.0117
263.26110.1035-1.70193.06122.10627.57180.01520.1647-0.02850.0517-0.10220.18550.0447-0.41370.02520.10360.0218-0.0280.21140.00460.156.454-11.8843-113.6384
271.29390.01210.78680.85210.92662.25810.01020.2626-0.05580.02990.01740.0623-0.0116-0.0728-0.08960.2143-0.0173-0.00030.23360.00910.211116.6884-11.0662-110.6794
282.5842-0.16651.20181.10640.1062.4077-0.16660.09050.38590.05150.05-0.2357-0.14040.02190.1370.1439-0.00660.0020.1569-0.00880.240834.7919-1.5054-93.7242
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 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 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 62 )
9X-RAY DIFFRACTION9chain 'B' and (resid 63 through 89 )
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 142 )
11X-RAY DIFFRACTION11chain 'B' and (resid 143 through 218 )
12X-RAY DIFFRACTION12chain 'B' and (resid 219 through 233 )
13X-RAY DIFFRACTION13chain 'B' and (resid 234 through 260 )
14X-RAY DIFFRACTION14chain 'B' and (resid 261 through 289 )
15X-RAY DIFFRACTION15chain 'B' and (resid 290 through 327 )
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 89 )
17X-RAY DIFFRACTION17chain 'C' and (resid 90 through 142 )
18X-RAY DIFFRACTION18chain 'C' and (resid 143 through 218 )
19X-RAY DIFFRACTION19chain 'C' and (resid 219 through 260 )
20X-RAY DIFFRACTION20chain 'C' and (resid 261 through 330 )
21X-RAY DIFFRACTION21chain 'D' and (resid 3 through 31 )
22X-RAY DIFFRACTION22chain 'D' and (resid 32 through 62 )
23X-RAY DIFFRACTION23chain 'D' and (resid 63 through 89 )
24X-RAY DIFFRACTION24chain 'D' and (resid 90 through 142 )
25X-RAY DIFFRACTION25chain 'D' and (resid 143 through 233 )
26X-RAY DIFFRACTION26chain 'D' and (resid 234 through 260 )
27X-RAY DIFFRACTION27chain 'D' and (resid 261 through 289 )
28X-RAY DIFFRACTION28chain 'D' and (resid 290 through 330 )

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