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- PDB-3ovq: Crystal Structure of hRPE and D-Ribulose-5-Phospate Complex -

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Basic information

Entry
Database: PDB / ID: 3ovq
TitleCrystal Structure of hRPE and D-Ribulose-5-Phospate Complex
ComponentsRibulose-phosphate 3-epimerasePhosphopentose epimerase
KeywordsISOMERASE / D-Ribulose-5-Phosphate
Function / homology
Function and homology information


ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / Pentose phosphate pathway / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / carbohydrate metabolic process / protein homodimerization activity / extracellular exosome / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Ribulose-phosphate 3-epimerase / Ribulose-phosphate 3-epimerase family signature 2. / Ribulose-phosphate 3-epimerase family signature 1. / Ribulose-phosphate 3-epimerase-like / Ribulose-phosphate 3 epimerase family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / : / Ribulose-phosphate 3-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsLiang, W.G. / Ouyang, S.Y. / Shaw, N. / Joachimiak, A. / Zhang, R.G. / Liu, Z.J.
CitationJournal: Faseb J. / Year: 2011
Title: Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE
Authors: Liang, W.G. / Ouyang, S.Y. / Shaw, N. / Joachimiak, A. / Zhang, R.G. / Liu, Z.J.
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Ribulose-phosphate 3-epimerase
B: Ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,69113
Polymers49,9092
Non-polymers3,78211
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.785, 43.535, 72.269
Angle α, β, γ (deg.)90.00, 94.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribulose-phosphate 3-epimerase / Phosphopentose epimerase / D-Ribulose-5-Phosphate 3-Epimerase


Mass: 24954.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPE, HUSSY-17 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96AT9, ribulose-phosphate 3-epimerase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE / Ribulose 5-phosphate


Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#4: Chemical
ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL / Polyethylene glycol


Mass: 458.541 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.94 Å3/Da / Density % sol: 36.61 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Sodium choride, 0.1M BIS-TRIS, 25%(w/v) Polyethylene glycol 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 35837 / Num. obs: 35837 / % possible obs: 99.9 % / Observed criterion σ(I): 6.7

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OVP

3ovp


Resolution: 1.999→25.939 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8959 / SU ML: 0.23 / σ(F): 0.12 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 1324 5.08 %
Rwork0.1472 --
obs0.1495 26067 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.225 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 95.23 Å2 / Biso mean: 31.9733 Å2 / Biso min: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.1534 Å20 Å21.7322 Å2
2--5.2555 Å20 Å2
3----3.1021 Å2
Refinement stepCycle: LAST / Resolution: 1.999→25.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 99 154 3579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073832
X-RAY DIFFRACTIONf_angle_d1.0335213
X-RAY DIFFRACTIONf_chiral_restr0.07559
X-RAY DIFFRACTIONf_plane_restr0.005695
X-RAY DIFFRACTIONf_dihedral_angle_d16.2611522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9991-2.07910.19531340.12552675280998
2.0791-2.17370.19821200.12442752287299
2.1737-2.28820.18041450.1292742288799
2.2882-2.43150.17681390.13482718285799
2.4315-2.6190.20741370.14327372874100
2.619-2.88230.19751620.154627502912100
2.8823-3.29870.21031700.164227432913100
3.2987-4.15320.17421470.134127802927100
4.1532-25.94140.18091700.150928463016100
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)
10.4362-0.37110.00990.7918-0.13160.01480.35850.29650.4287-0.3498-0.13610.34620.1723-0.17030.00480.2098-0.07240.03950.3462-0.05390.256418.09828.385726.2648
20.57240.2121-0.710.4228-0.64261.01190.0426-0.0869-0.1117-0.0009-0.0109-0.0803-0.09560.15150.00010.1998-0.02620.00070.2282-0.00430.208418.41664.179318.042
30.1111-0.0156-0.03470.37-0.28810.2188-0.0827-0.113-0.3484-0.0378-0.0322-0.3186-0.00340.38670.00010.23270.0113-0.01480.32880.03490.339826.306-3.13921.4499
40.69650.19960.10390.3706-0.34672.0477-0.0068-0.0478-0.33490.0094-0.008-0.10850.4122-0.0058-00.2193-0.0175-0.0010.14320.03210.20298.6227-7.768924.8536
50.9864-0.1381-0.84530.62950.5691.92540.1148-0.34950.17110.2654-0.03780.0115-0.31250.013900.2701-0.02270.0120.2216-0.01080.19666.29116.689133.3916
60.0436-0.119-0.00480.32260.0090.11480.09340.52320.7112-0.42140.4214-0.6951-1.20160.870.0130.5879-0.24410.14870.4211-0.02070.376122.634517.735322.6764
7-0.0155-0.0158-0.00060.0256-0.03640.0148-0.0238-1.3308-0.05860.78360.0898-0.28980.0148-0.5123-0.00020.5153-0.0861-0.04380.8159-0.14450.398519.159514.784537.9134
80.096-0.0231-0.26540.011-0.12352.158-0.3298-0.3503-0.14030.2086-0.0299-0.43030.60580.135-0.02270.1807-0.0014-0.01620.2693-0.0220.152923.3509-2.4559-8.2385
90.1173-0.06230.08290.0619-0.10080.15440.1165-0.0018-0.281-0.0029-0.1487-0.1710.15040.19860.00010.2113-0.04940.00670.2960.01110.26928.01111.75921.9138
100.269-0.00510.49680.77620.68671.39-0.01440.04080.1544-0.07570.0728-0.0165-0.07230.108300.1322-0.00570.00670.1542-0.00160.197415.29792.52071.4561
111.4309-0.07690.00441.2858-0.2241.039-0.00730.0970.0874-0.11440.02340.10650.0031-0.154300.12670.0106-0.0240.14960.02080.1555.3237-1.5104-7.3063
121.76840.3674-0.0640.92930.63260.492-0.10920.0584-0.2493-0.07070.1262-0.22140.20850.1947-0.00010.23490.01080.00960.2672-0.01840.247717.7345-12.3696-12.6692
130.0841-0.2037-0.07360.5037-0.06770.2002-0.14180.21910.0466-0.0023-0.0212-0.3981-0.37290.74640.00020.28370.04110.02980.3143-0.02890.400331.9658-4.7137-10.4066
140.0766-0.1233-0.05720.18690.10880.11540.30320.01790.5785-0.5044-0.059-0.7317-0.47160.31920.0080.52930.1737-0.11010.3710.03010.310525.5941-8.7485-25.6814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:14)A4 - 14
2X-RAY DIFFRACTION2(chain A and resid 15:52)A15 - 52
3X-RAY DIFFRACTION3(chain A and resid 53:68)A53 - 68
4X-RAY DIFFRACTION4(chain A and resid 69:125)A69 - 125
5X-RAY DIFFRACTION5(chain A and resid 126:197)A126 - 197
6X-RAY DIFFRACTION6(chain A and resid 198:208)A198 - 208
7X-RAY DIFFRACTION7(chain A and resid 209:222)A209 - 222
8X-RAY DIFFRACTION8(chain B and resid 5:11)B5 - 11
9X-RAY DIFFRACTION9(chain B and resid 12:31)B12 - 31
10X-RAY DIFFRACTION10(chain B and resid 32:75)B32 - 75
11X-RAY DIFFRACTION11(chain B and resid 76:143)B76 - 143
12X-RAY DIFFRACTION12(chain B and resid 144:199)B144 - 199
13X-RAY DIFFRACTION13(chain B and resid 200:218)B200 - 218
14X-RAY DIFFRACTION14(chain B and resid 219:223)B219 - 223

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