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- PDB-4zqb: Crystal structure of NADP-dependent dehydrogenase from Rhodobacte... -

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Basic information

Entry
Database: PDB / ID: 4zqb
TitleCrystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate
ComponentsNADP-dependent dehydrogenase
KeywordsOXIDOREDUCTASE / 2-hydroxyacid dehydrogenase / NADP / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKowiel, M. / Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Porebski, P.J. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate
Authors: Kowiel, M. / Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Porebski, P.J. / Bonanno, J. / Almo, S.C. / Minor, W.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent dehydrogenase
B: NADP-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,78411
Polymers68,5642
Non-polymers2,2199
Water12,502694
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADP-dependent dehydrogenase
hetero molecules

A: NADP-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,78411
Polymers68,5642
Non-polymers2,2199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
Buried area8240 Å2
ΔGint-92 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.489, 71.489, 244.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 312 / Label seq-ID: 4 - 315

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NADP-dependent dehydrogenase


Mass: 34282.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_3442 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q3IWN8, glyoxylate reductase (NADP+), hydroxypyruvate reductase

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Non-polymers , 6 types, 703 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 10.5 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition # 23 (0.1M Bis-Tris, ...Details: 0.2 ul of 10.5 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition # 23 (0.1M Bis-Tris, 25%w/v PEG 3350, 0.2M Li sulfate pH=6.5 ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin and 10 mM NADP solution at 289 K for 3 hours.
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 60347 / Num. obs: 59896 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.073 / Rrim(I) all: 0.171 / Rsym value: 0.161 / Χ2: 1.422 / Net I/av σ(I): 15.323 / Net I/σ(I): 4.7 / Num. measured all: 368480
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.85-1.886.2229550.6490.4280.88497.1
1.88-1.926.328990.7070.3990.93397.50.943
1.92-1.956.429890.7760.3370.98198.60.8010.87
1.95-1.996.430110.7880.2981.03599.80.7050.767
1.99-2.046.530130.8340.2751.0741000.6510.708
2.04-2.086.529740.8360.2551.0721000.6030.656
2.08-2.146.530010.8780.2211.1821000.5210.567
2.14-2.196.530240.8830.1931.18399.90.4530.494
2.19-2.266.530320.9210.1671.28799.90.3930.428
2.26-2.336.429650.9330.151.34499.90.3530.385
2.33-2.416.430190.9390.1351.35199.90.3140.342
2.41-2.516.330110.9490.1171.46599.90.2720.297
2.51-2.636.330110.9630.1021.599.80.2360.258
2.63-2.766.230140.9710.0861.6499.70.1980.216
2.76-2.94629800.9770.0741.74699.70.1660.182
2.94-3.165.930140.9830.0631.90399.60.1410.155
3.16-3.485.729940.9880.0481.98599.40.1050.116
3.48-3.995.430200.990.0392.146990.080.089
3.99-5.025.129650.9940.0322.0298.40.0640.071
5.02-505.530050.9950.032.26997.30.0650.072

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
Cootmodel building
REFMAC5.8.0107refinement
HKL-3000phasing
MOLREPphasing
HKL-3000data scaling
HKL-3000data reduction
BLU-MAXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP8

3pp8


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1819 / WRfactor Rwork: 0.1493 / FOM work R set: 0.8401 / SU B: 6.073 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1266 / SU Rfree: 0.1189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.119 / SU Rfree Cruickshank DPI: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 2948 4.9 %RANDOM
Rwork0.1649 56677 --
obs0.1665 59625 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.24 Å2 / Biso mean: 27.931 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å2-0 Å2
2---0.35 Å20 Å2
3---1.15 Å2
Refinement stepCycle: final / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 139 694 5595
Biso mean--25.48 35.5 -
Num. residues----629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195089
X-RAY DIFFRACTIONr_bond_other_d0.0070.024868
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9966983
X-RAY DIFFRACTIONr_angle_other_deg1.263311165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83621.98202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20515752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.481551
X-RAY DIFFRACTIONr_chiral_restr0.0850.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215663
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021134
X-RAY DIFFRACTIONr_mcbond_it0.5841.512534
X-RAY DIFFRACTIONr_mcbond_other0.5851.512533
X-RAY DIFFRACTIONr_mcangle_it0.9382.2623169
Refine LS restraints NCS

Ens-ID: 1 / Number: 36980 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 228 -
Rwork0.275 4047 -
all-4275 -
obs--97.29 %
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)
14.2367-0.5755-1.80852.2388-0.87674.1427-0.16950.1514-0.6202-0.1382-0.10710.42110.4894-0.310.27670.0625-0.03370.00740.0392-0.05840.2584-34.489-15.30820.511
23.3479-0.67773.83631.4194-0.012510.28780.0182-0.2586-0.31790.0690.09240.23410.172-0.3091-0.11070.0188-0.00680.03180.02540.01660.1817-38.066-11.83525.616
31.0147-0.0020.40322.1908-0.40160.8559-0.0392-0.02980.0149-0.01370.04790.20930.1148-0.1185-0.00880.0550.0076-0.02820.0439-0.02760.1958-36.537-6.08615.892
40.2946-0.49910.07180.8744-0.05940.16760.01070.01170.0389-0.0322-0.0201-0.0444-0.02870.01080.00930.05360.0247-0.03030.0258-0.02350.2094-13.861-16.42314.5
52.46941.66230.90797.93932.02551.1646-0.01460.1651-0.095-0.32520.1658-0.5105-0.04040.2867-0.15120.0320.02470.02280.124-0.02270.08486.535-34.46211.511
61.874-1.54720.37791.7642-0.47260.8109-0.0455-0.09840.1460.0020.0632-0.1458-0.13680.0604-0.01770.0513-0.0058-0.04440.0161-0.02340.2348-0.897-13.01917.149
71.549-1.9764-1.55396.4455-1.52085.0090.02490.05830.26110.32330.0456-0.3149-0.4571-0.0611-0.07060.0817-0.039-0.03940.06250.030.28010.623-3.33312.497
82.996-1.758-0.43422.276-0.20271.0723-0.0227-0.00020.1771-0.05570.0608-0.1673-0.10990.1248-0.03820.0421-0.0184-0.02590.0355-0.01640.2368-2.843-12.1217.749
94.7575-2.135-3.27392.7110.61723.13010.2170.16280.4273-0.1617-0.0536-0.2699-0.39590.0538-0.16350.1817-0.096-0.01720.0820.04250.1999-3.756-10.487-0.683
100.7284-0.14050.20960.6070.11570.792-0.01250.12840.064-0.05030.04240.0099-0.0050.1057-0.02980.05270.0131-0.03210.0431-0.00790.1947-10.712-22.4043.117
111.4499-0.6879-0.67910.69540.58010.7134-0.0526-0.14940.12340.04740.0559-0.0505-0.0150.0449-0.00330.04890.021-0.03150.0222-0.02060.1953-24.908-2.59223.188
126.3132-6.90665.907315.3494-5.05415.78330.31240.2194-0.1537-0.3835-0.1128-0.10180.30140.2367-0.19950.30940.07580.03210.2084-0.00270.4991-16.294-60.276-11.382
134.4191-1.5268-2.11763.97341.17361.98850.26570.751-0.3083-0.436-0.19950.0898-0.1335-0.1152-0.06620.12260.0535-0.04910.1923-0.09420.1785-24.461-43.407-22.892
1411.54674.0442-0.66123.42671.45933.5048-0.3820.2143-0.3701-0.54950.339-0.30850.0560.4880.0430.19870.02060.03040.1102-0.04870.2502-16.85-48.398-18.415
150.8822-0.0013-0.13774.14491.13690.72580.01320.2023-0.34790.0722-0.0890.12870.10510.0240.07580.12850.0025-0.0390.0689-0.06380.3037-27.917-49.9-14.042
160.1574-0.10540.0850.9884-0.69010.48670.02790.0469-0.0212-0.0616-0.01010.04970.0480.0142-0.01790.0846-0.0127-0.0380.02930.0080.1904-31.308-21.728-17.857
170.3165-0.3182-0.12462.3032-1.35031.18290.00090.00480.01660.1223-0.0043-0.002-0.0622-0.00650.00340.0611-0.017-0.04880.01690.01010.1923-30.184-8.211-11.653
183.03022.6366-2.40373.52-3.48395.01-0.0893-0.02220.04750.0243-0.0178-0.10.0529-0.00290.10720.05560.0022-0.03780.0022-0.01480.1336-29.909-13.738-4.173
194.6609-0.49160.46431.6002-0.42790.688-0.0013-0.1356-0.15120.1283-0.0208-0.01770.1056-0.06730.0220.0792-0.0145-0.00910.0145-0.01050.1711-35.401-14.4790.695
201.8157-0.3803-0.18123.4843-0.01150.89250.00310.01890.02370.0974-0.04310.1236-0.0109-0.08110.040.0418-0.0043-0.03320.02760.00560.122-42.407-17.446-8.377
210.7263-0.16390.13630.95040.00350.5118-0.0309-0.03040.0249-0.05440.01980.03730.0445-0.10350.01120.0534-0.0266-0.03970.03720.02220.1768-41.909-19.466-20.93
222.2706-1.99430.78383.0602-0.86091.38430.0685-0.1618-0.06410.04990.0172-0.09560.17360.2585-0.08580.11870.0167-0.08420.1074-0.00510.2246-21.722-39.355-6.889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 36
3X-RAY DIFFRACTION3A37 - 71
4X-RAY DIFFRACTION4A72 - 122
5X-RAY DIFFRACTION5A123 - 137
6X-RAY DIFFRACTION6A138 - 167
7X-RAY DIFFRACTION7A168 - 186
8X-RAY DIFFRACTION8A187 - 203
9X-RAY DIFFRACTION9A204 - 218
10X-RAY DIFFRACTION10A219 - 282
11X-RAY DIFFRACTION11A283 - 313
12X-RAY DIFFRACTION12B-2 - 3
13X-RAY DIFFRACTION13B4 - 23
14X-RAY DIFFRACTION14B24 - 34
15X-RAY DIFFRACTION15B35 - 73
16X-RAY DIFFRACTION16B74 - 127
17X-RAY DIFFRACTION17B128 - 155
18X-RAY DIFFRACTION18B156 - 170
19X-RAY DIFFRACTION19B171 - 190
20X-RAY DIFFRACTION20B191 - 219
21X-RAY DIFFRACTION21B220 - 281
22X-RAY DIFFRACTION22B282 - 313

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