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- PDB-2rcy: Crystal structure of Plasmodium falciparum pyrroline carboxylate ... -

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Basic information

Entry
Database: PDB / ID: 2rcy
TitleCrystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound
ComponentsPyrroline carboxylate reductase
KeywordsOXIDOREDUCTASE / malaria / structural genomics / pyrroline reductase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Glutamate and glutamine metabolism / pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / : / nucleotide binding
Similarity search - Function
ProC C-terminal domain-like / ProC C-terminal domain-like fold / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...ProC C-terminal domain-like / ProC C-terminal domain-like fold / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pyrroline-5-carboxylate reductase, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWernimont, A.K. / Lew, J. / Lin, Y.H. / Ren, H. / Sun, X. / Khuu, C. / Hassanali, A. / Wasney, G. / Zhao, Y. / Kozieradzki, I. ...Wernimont, A.K. / Lew, J. / Lin, Y.H. / Ren, H. / Sun, X. / Khuu, C. / Hassanali, A. / Wasney, G. / Zhao, Y. / Kozieradzki, I. / Schapira, M. / Bochkarev, A. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Artz, J.D. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound.
Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Ren, H. / Sun, X. / Khuu, C. / Hassanali, A. / Zhao, Y. / Kozieradzki, I. / Schapira, M. / Bochkarev, A. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. ...Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Ren, H. / Sun, X. / Khuu, C. / Hassanali, A. / Zhao, Y. / Kozieradzki, I. / Schapira, M. / Bochkarev, A. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Artz, J.D. / Amani, M.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_seq_id / _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: Pyrroline carboxylate reductase
B: Pyrroline carboxylate reductase
C: Pyrroline carboxylate reductase
D: Pyrroline carboxylate reductase
E: Pyrroline carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,03216
Polymers144,0345
Non-polymers3,99811
Water7,692427
1
A: Pyrroline carboxylate reductase
B: Pyrroline carboxylate reductase
C: Pyrroline carboxylate reductase
D: Pyrroline carboxylate reductase
E: Pyrroline carboxylate reductase
hetero molecules

A: Pyrroline carboxylate reductase
B: Pyrroline carboxylate reductase
C: Pyrroline carboxylate reductase
D: Pyrroline carboxylate reductase
E: Pyrroline carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,06532
Polymers288,06810
Non-polymers7,99722
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area61100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.207, 113.741, 82.651
Angle α, β, γ (deg.)90.000, 105.710, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61A
71B
81C
91D
101E
111A
121B
131C
141D
151E
161A
171B
181C
191D
201E
211A
221B
231C
241D
251E
12B
22A
32D
42C
52E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNASNASN4AA4 - 274 - 27
211ASNASNASNASN4BB4 - 274 - 27
311ASNASNASNASN4CC4 - 274 - 27
411ILEILEASNASN4DD5 - 275 - 27
511LEULEUASNASN7EE7 - 277 - 27
621LEULEULYSLYS1AA34 - 4234 - 42
721LEULEULYSLYS1BB34 - 4234 - 42
821LEULEULYSLYS1CC34 - 4234 - 42
921LEULEULYSLYS1DD34 - 4234 - 42
1021LEULEULYSLYS1EE34 - 4234 - 42
1131THRTHRGLUGLU1AA44 - 5344 - 53
1231THRTHRGLUGLU1BB44 - 5344 - 53
1331THRTHRGLUGLU1CC44 - 5344 - 53
1431THRTHRGLUGLU1DD44 - 5344 - 53
1531THRTHRGLUGLU1EE44 - 5344 - 53
1641ILEILEGLYGLY4AA62 - 10462 - 104
1741ILEILEGLYGLY4BB62 - 10462 - 104
1841ILEILEGLYGLY4CC62 - 10462 - 104
1941ILEILEGLYGLY4DD62 - 10462 - 104
2041ILEILEGLYGLY4EE62 - 10462 - 104
2151VALVALSERSER4AA110 - 262110 - 262
2251VALVALSERSER4BB110 - 262110 - 262
2351VALVALSERSER4CC110 - 262110 - 262
2451VALVALSERSER4DD110 - 262110 - 262
2551VALVALSERSER4EE110 - 262110 - 262
112NAPNAPNAPNAP264BJ264
212NAPNAPNAPNAP264AG264
312NAPNAPNAPNAP264DN264
412NAPNAPNAPNAP264CL264
512NAPNAPNAPNAP264EP264

NCS ensembles :
ID
1
2
DetailsDecamer - five-fold ring of dimers

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Components

#1: Protein
Pyrroline carboxylate reductase


Mass: 28806.787 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: MAL13P1.284 / Plasmid: p15-tev-lic / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: Q8IDC6, pyrroline-5-carboxylate reductase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG MME550, 50 mM MgCl2, 0.1 M Hepes pH 7.5, 5 mM NADP, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.3→46.27 Å / Num. all: 57815 / Num. obs: 57815 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.142 / Rsym value: 0.108 / Χ2: 3.221 / Net I/σ(I): 7.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.1 / Num. unique all: 3416 / Rsym value: 0.721 / Χ2: 1.076 / % possible all: 53.6

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.74 / FOM acentric: 0.72 / FOM centric: 1.28 / Reflection: 57316 / Reflection acentric: 55502 / Reflection centric: 1814
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-34.8620.920.920.8827762553223
4.1-6.60.880.890.8484448081363
3.3-4.10.920.833.611059410262332
2.9-3.30.740.740.741062810344284
2.5-2.90.610.60.741827117844427
2.3-2.50.540.540.5666036418185

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVE2.11phasing
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→46.27 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.831 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.527 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2849 5.1 %RANDOM
Rwork0.245 ---
obs0.247 56209 88.86 %-
all-56209 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.213 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.05 Å2
2--0.06 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 256 427 10079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229817
X-RAY DIFFRACTIONr_angle_refined_deg0.9412.00813298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8851259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72726.696342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.542151708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.407157
X-RAY DIFFRACTIONr_chiral_restr0.0540.21545
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027046
X-RAY DIFFRACTIONr_nbd_refined0.1660.25261
X-RAY DIFFRACTIONr_nbtor_refined0.2850.26946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.2530
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.2217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.228
X-RAY DIFFRACTIONr_mcbond_it0.2261.56459
X-RAY DIFFRACTIONr_mcangle_it0.403210030
X-RAY DIFFRACTIONr_scbond_it0.2933850
X-RAY DIFFRACTIONr_scangle_it0.4624.53266
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeWeight positionRms dev position (Å)
11A140TIGHT POSITIONAL0.05
12B140TIGHT POSITIONAL0.050.01
13C140TIGHT POSITIONAL0.050.01
14D140TIGHT POSITIONAL0.050.01
15E140TIGHT POSITIONAL0.05
11A1565MEDIUM POSITIONAL0.50.21
12B1565MEDIUM POSITIONAL0.50.23
13C1565MEDIUM POSITIONAL0.50.21
14D1565MEDIUM POSITIONAL0.50.2
15E1565MEDIUM POSITIONAL0.50.21
11A140TIGHT THERMAL0.50.01
12B140TIGHT THERMAL0.50.01
13C140TIGHT THERMAL0.50.02
14D140TIGHT THERMAL0.50.01
15E140TIGHT THERMAL0.50.01
11A1565MEDIUM THERMAL20.09
12B1565MEDIUM THERMAL20.08
13C1565MEDIUM THERMAL20.11
14D1565MEDIUM THERMAL20.13
15E1565MEDIUM THERMAL20.09
22A48MEDIUM POSITIONAL0.50.46
22B48MEDIUM POSITIONAL0.50.13
22D48MEDIUM POSITIONAL0.50.12
22A48MEDIUM POSITIONAL0.50.15
22B48MEDIUM POSITIONAL0.50.13
22A48MEDIUM THERMAL20.22
22B48MEDIUM THERMAL20.17
22D48MEDIUM THERMAL20.16
22A48MEDIUM THERMAL20.23
22B48MEDIUM THERMAL20.09
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 116 -
Rwork0.324 2015 -
all-2131 -
obs-3137 45.56 %

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