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- PDB-3hwr: Crystal structure of PanE/ApbA family ketopantoate reductase (YP_... -

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Basic information

Entry
Database: PDB / ID: 3hwr
TitleCrystal structure of PanE/ApbA family ketopantoate reductase (YP_299159.1) from Ralstonia eutropha JMP134 at 2.15 A resolution
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / YP_299159.1 / PanE/ApbA family ketopantoate reductase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / NADP / Pantothenate biosynthesis
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / nucleotide binding
Similarity search - Function
Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of PanE/ApbA family ketopantoate reductase (YP_299159.1) from Ralstonia eutropha JMP134 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 2-dehydropantoate 2-reductase
B: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8658
Polymers68,8122
Non-polymers2,0546
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-21 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.210, 116.210, 95.604
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 298
2115B1 - 298

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Components

#1: Protein 2-dehydropantoate 2-reductase / PanE/ApbA family ketopantoate reductase


Mass: 34405.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_B4967, YP_299159.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46RB9, 2-dehydropantoate 2-reductase
#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: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY THE TARGET ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS AN ARGININE AT POSITION 244 INSTEAD OF A GLYCINE. THE ARGININE AT POSITION 244 IS SUPPORTED BY THE ELECTRON DENSITY. THE AUTHORS DO NOT KNOW IF THIS GLY TO ARG DIFFERENCE IS DUE TO AN ERROR IN THE DB SEQUENCE, A MUTATION IN THE GENOMIC DNA (SAME SOURCE STRAIN AS USED FOR GENOME SEQUENCING) OR A MUTATION INTRODUCED BY PCR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.7154.58THE STRUCTURE WAS SOLVED BY 3-WAVELENGTH MAD METHOD USING 2.4 A DATA FROM ANOTHER CRYSTAL. THESE PHASES WERE USED AS RESTRAINTS IN THE CURRENT REFINEMENT.
2
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.71
Details: 26.2000% polyethylene glycol 6000, 0.1M Bicine pH 8.71, Additive: 0.001 M dihydro-nicotinamide-adenine-dinucleotide phosphate (NADPH), VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.91837
SYNCHROTRONSSRL BL9-220.97927,0.91162,0.97912
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJan 28, 2009Flat mirror, vertical and horizontal focussing mirrors
MARMOSAIC 325 mm CCD2CCDJan 9, 2009Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979271
30.911621
40.979121
ReflectionResolution: 2.15→29.761 Å / Num. obs: 39885 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.533 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 4.124
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.213.80.71911097529230.719100
2.21-2.273.70.7090.41048228420.709100
2.27-2.333.70.5321.11054728140.532100
2.33-2.43.80.4271.71012426910.427100
2.4-2.483.80.3731.9990726300.373100
2.48-2.573.80.3062.3958325410.306100
2.57-2.673.80.2472.5928324690.247100
2.67-2.783.80.2221.7889623710.222100
2.78-2.93.80.1664.1858522770.166100
2.9-3.043.80.1375.1806421390.137100
3.04-3.213.80.1185.9780520780.118100
3.21-3.43.80.1016.2729219420.101100
3.4-3.633.70.0914.3685318430.091100
3.63-3.933.70.0815.4637617140.081100
3.93-4.33.70.0659.5597715950.065100
4.3-4.813.80.06110531414170.061100
4.81-5.553.70.0659.5473612700.065100
5.55-6.83.70.0738.2393910700.073100
6.8-9.623.70.0649.130408320.06499.1
9.62-29.763.40.0591014524270.05991.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.761 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.62 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.177
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4.NADPH,DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, (NDP) WAS MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH SUBUNIT IN THE ASYMMETRIC UNIT. 5. BICINE (BCN) AND (4R)-2-METHYLPENTANE-2,4-DIOL (MRD) FROM THE CRYSTALLIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2003 5 %RANDOM
Rwork0.183 ---
obs0.186 39845 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.48 Å2 / Biso mean: 49.293 Å2 / Biso min: 21.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0.7 Å20 Å2
2---1.4 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 134 213 4708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224711
X-RAY DIFFRACTIONr_bond_other_d0.0020.023103
X-RAY DIFFRACTIONr_angle_refined_deg1.7812.0016448
X-RAY DIFFRACTIONr_angle_other_deg1.28537606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3285642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55723.222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18415762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8981542
X-RAY DIFFRACTIONr_chiral_restr0.090.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02891
X-RAY DIFFRACTIONr_nbd_refined0.1940.3935
X-RAY DIFFRACTIONr_nbd_other0.1770.33180
X-RAY DIFFRACTIONr_nbtor_refined0.1640.52209
X-RAY DIFFRACTIONr_nbtor_other0.0870.52410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5295
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2520.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.363
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.514
X-RAY DIFFRACTIONr_mcbond_it1.91833357
X-RAY DIFFRACTIONr_mcbond_other0.48731245
X-RAY DIFFRACTIONr_mcangle_it2.68954851
X-RAY DIFFRACTIONr_scbond_it5.11781782
X-RAY DIFFRACTIONr_scangle_it6.855111574
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1754MEDIUM POSITIONAL0.150.5
1856LOOSE POSITIONAL0.365
1754MEDIUM THERMAL0.712
1856LOOSE THERMAL1.710
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 140 -
Rwork0.265 2782 -
all-2922 -
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)
11.85390.12310.31161.6132-0.61541.40360.1973-0.2997-0.66020.12150.08620.0020.42360.0012-0.2835-0.08320.0078-0.1563-0.21880.07670.027767.28763.139-14.482
21.81630.7830.10792.13170.46720.3461-0.02660.4103-0.2504-0.41510.2414-0.6069-0.09890.3163-0.2147-0.1736-0.03640.12990.0093-0.1567-0.028494.9688.314-40.751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 299
2X-RAY DIFFRACTION2B1 - 298

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