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- PDB-3ovr: Crystal Structure of hRPE and D-Xylulose 5-Phosphate Complex -

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Basic information

Entry
Database: PDB / ID: 3ovr
TitleCrystal Structure of hRPE and D-Xylulose 5-Phosphate Complex
ComponentsRibulose-phosphate 3-epimerase
KeywordsISOMERASE / D-Xylulose 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
5-O-phosphono-D-xylulose / : / Ribulose-phosphate 3-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.948 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 16, 2015Group: Other
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_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.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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.006, 43.665, 72.655
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribulose-phosphate 3-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-5SP / 5-O-phosphono-D-xylulose / D-xylulose 5-phosphate


Type: saccharide / 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


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


Mass: 18.015 Da / Num. of mol.: 252 / 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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Sodium Choloride, 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
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 38246 / Num. obs: 38246 / % possible obs: 98.6 % / Observed criterion σ(I): 11.7

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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: 1.948→25.223 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8962 / SU ML: 0.22 / σ(F): 0.11 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1918 1411 5.07 %
Rwork0.1441 --
obs0.1465 27840 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.898 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 87.1 Å2 / Biso mean: 23.2694 Å2 / Biso min: 6.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.8045 Å20 Å20.7446 Å2
2--2.1237 Å20 Å2
3----0.3191 Å2
Refinement stepCycle: LAST / Resolution: 1.948→25.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 104 252 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063818
X-RAY DIFFRACTIONf_angle_d1.0175189
X-RAY DIFFRACTIONf_chiral_restr0.07556
X-RAY DIFFRACTIONf_plane_restr0.005688
X-RAY DIFFRACTIONf_dihedral_angle_d16.6051519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9485-2.01810.21451410.14012474261592
2.0181-2.09880.20071210.13042601272296
2.0988-2.19430.17371370.1252583272096
2.1943-2.30990.19291450.12782604274996
2.3099-2.45450.18351200.12922617273797
2.4545-2.64390.19161420.13412653279598
2.6439-2.90960.21021360.14662692282898
2.9096-3.32980.20861520.15232672282499
3.3298-4.1920.15911580.133727382896100
4.192-25.22480.18161590.153127952954100
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)
10.12550.1143-0.19860.1199-0.14320.59380.3914-0.27230.341-0.17210.15140.1645-0.00840.02650.02090.1693-0.11080.02570.2705-0.05770.139219.48947.452533.7488
20.02330.01010.02920.00810.00960.02050.23160.16570.1044-0.010.0578-0.3944-0.3402-0.1298-0.00020.1652-0.02630.02330.1923-0.00970.166419.97538.590814.3828
30.43190.3012-0.57570.088-0.33370.59940.0610.0414-0.11990.0231-0.01940.0206-0.09050.10250.00030.1018-0.0101-0.0030.1248-0.01270.109517.82344.562919.3598
40.00520.0050.028-0.0143-0.01240.09410.10270.1042-0.1056-0.1473-0.0454-0.21820.30270.5171-0.00010.13530.01030.00050.2013-0.01720.21125.7593-3.713216.235
50.01060.0081-0.00770.00640.00560.0097-0.11890.20050.11080.0774-0.3756-0.76070.06280.5636-0.00120.1660.0339-0.02880.29870.04720.35728.0303-3.786426.9044
60.06280.1863-0.09710.4228-0.38220.7178-0.0278-0.0749-0.20.03940.0246-0.0570.3392-0.027700.1647-0.00540.00140.1155-0.00330.132910.2738-7.115321.8571
70.20180.01550.31920.03070.00720.52380.17410.0726-0.6718-0.33050.22020.46660.48880.28180.01030.2702-0.0654-0.00450.14590.09770.26065.1545-13.855929.2047
80.28380.18480.24640.202-0.02840.65820.1511-0.0198-0.16020.0024-0.04130.01010.1438-0.0394-0.00010.1470.0048-0.01850.13060.03530.12858.2009-5.955929.3018
92.1624-0.56440.37870.3762-0.17150.0965-0.1261-0.26070.70530.18-0.07860.01460.0097-0.3001-0.01670.2414-0.04210.02880.26410.01420.136-0.7671-4.65935.8329
100.2345-0.0329-0.2030.04130.07360.27030.0927-0.170.0689-0.0378-0.1481-0.0356-0.06970.0373-0.00020.14390.0120.0030.11210.02520.11746.81173.010427.5489
110.02090.03360.00370.03650.0021-0.0010.1981-0.0626-0.2422-0.0052-0.00090.1343-0.5776-0.20260.00060.30640.01140.04170.0851-0.02960.19854.079415.936224.8455
120.0293-0.1299-0.0160.0840.04080.113-0.0818-0.14930.00610.01210.12360.0071-0.0609-0.35730.00010.2060.00780.03340.1891-0.0080.11542.2167.573738.3145
130.67590.2366-0.10850.1078-0.00210.19260.1719-0.3660.19090.2483-0.194-0.0036-0.41270.1303-0.00120.2376-0.03660.02060.1689-0.03390.163510.582410.959635.6067
140.0293-0.0435-0.04830.04840.05560.04890.1525-0.35210.176-0.03620.0994-0.0898-0.38910.16430.00010.1775-0.04750.01350.1538-0.00910.109915.31199.174828.9874
150.05540.0085-0.14980.34090.60871.5730.17460.35840.3493-0.16820.3670.15170.50210.19130.02020.4894-0.24050.08040.25690.00630.333622.086719.032521.9829
161.3882-0.54440.28490.3025-0.11710.0539-0.065-1.25640.46370.22270.0554-0.427-0.7476-0.0376-0.00730.2582-0.08390.01150.3395-0.11280.304223.887415.832332.2951
170.00160.00760.00410.02480.01630.01210.4056-0.0088-0.29190.18950.1072-0.1323-0.1058-0.2463-0.00030.4154-0.0034-0.1150.3893-0.15110.380117.066914.400740.9704
180.0062-0.00180.00760.00020.00110.0032-0.18460.0613-0.09750.00890.0123-0.1924-0.01880.01250.00010.6659-0.1212-0.11390.7178-0.14780.339813.386611.999346.9248
190.1830.03970.16680.16570.10430.1369-0.07440.21330.10680.0775-0.0764-0.31360.37380.0381-0.00480.14750.0078-0.01470.2116-0.01780.109823.2901-3.1686-6.7777
200.01870.05180.01570.04780.02090.00520.2231-0.04410.05830.1406-0.3411-0.3618-0.05790.486700.1468-0.04430.02780.2394-0.00520.207426.97781.09137.1566
210.0432-0.06640.00840.1441-0.00460.04650.14610.209-0.2001-0.1543-0.0465-0.0720.11640.06370.00040.1051-0.03310.00870.1582-0.01750.164728.00413.6883-4.3912
220.02890.00270.15670.2601-0.27780.60420.00070.01020.05220.03170.09370.08080.0868-0.03420.0070.0638-0.008-0.00280.088-0.01030.107913.3978-0.81425.5362
230.0261-0.0205-0.01490.05320.02930.01690.2978-0.10270.130.3-0.18030.0097-0.44650.4388-0.00030.1568-0.03630.02540.1990.01450.20622.099712.19761.4022
240.55860.3235-0.04050.3199-0.02230.5667-0.11620.2422-0.0018-0.04480.07610.0520.0034-0.148-0.00010.07920.0028-0.01010.07660.00950.079315.12394.1213-3.0179
250.0003-0.0066-0.00870.01430.0330.0497-0.0588-0.07190.2007-0.2939-0.25950.29410.1227-0.19340.00010.09890.02280.02080.1359-0.01270.15771.92171.24593.1123
260.9195-0.1613-0.28060.25840.11010.86570.00530.09130.11010.0020.0923-0.0102-0.0379-0.1135-0.00790.07030.0212-0.01470.07740.02010.11245.14021.4677-5.6667
270.0215-0.01260.0270.013-0.01160.01590.1511-0.4849-0.10870.0645-0.0204-0.03230.4084-0.37310.00020.1911-0.0180.00280.2113-0.00640.14472.7725-13.643-13.356
280.03260.0034-0.0208-0.00030.00580.0124-0.22740.26790.6316-0.66850.12730.0357-0.1587-0.15490.00020.208-0.0287-0.06440.1231-0.0080.16530.7004-4.0911-16.3925
290.2263-0.0402-0.12550.10150.08090.0972-0.0641-0.1276-0.13820.03320.10860.0706-0.0283-0.0067-0.0010.05340.0074-0.01250.09030.01190.104213.0423-9.3468-5.9701
300.0417-0.0087-0.01590.1925-0.130.0796-0.10950.1773-0.4143-0.02390.2461-0.27860.27810.51540.00030.15220.0117-0.00240.2024-0.05160.191918.0944-18.8173-8.9029
31-0.0036-0.00110.02590.0032-0.02160.0285-0.07520.4865-0.2859-0.63740.06820.07090.2629-0.0938-0.00050.1864-0.0193-0.00680.2318-0.01020.15529.9889-11.7098-20.6979
320.17940.16890.04040.14310.07190.1076-0.17760.20250.0923-0.0130.07-0.23330.01560.336800.13230.0194-0.00720.19410.00950.1419.8907-9.473-13.3293
330.2442-0.018-0.23760.1931-0.0390.2155-0.1492-0.0124-0.15860.08240.1202-0.16380.290.1408-00.15150.01290.01050.1538-0.01190.130421.9855-10.054-13.6898
342.04930.18910.1860.216-0.17290.2955-0.75560.79320.6947-0.1845-0.232-0.3046-0.16690.0038-0.01490.162-0.0709-0.07570.19260.05240.310334.5829-5.4728-1.1911
350.1556-0.1749-0.13180.18640.08510.12610.18170.25830.1005-0.2044-0.0563-0.2818-0.12880.2436-0.00020.17310.03680.04250.1828-0.01530.223130.9225-4.4337-13.8795
360.4575-0.3457-0.22570.26070.2120.83130.14760.31970.4846-0.6111-0.1229-0.0852-0.69260.24350.03460.26360.1381-0.08110.2396-0.03190.130925.7869-8.8826-25.8103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:9)A4 - 9
2X-RAY DIFFRACTION2(chain A and resid 10:19)A10 - 19
3X-RAY DIFFRACTION3(chain A and resid 20:50)A20 - 50
4X-RAY DIFFRACTION4(chain A and resid 51:62)A51 - 62
5X-RAY DIFFRACTION5(chain A and resid 63:66)A63 - 66
6X-RAY DIFFRACTION6(chain A and resid 67:99)A67 - 99
7X-RAY DIFFRACTION7(chain A and resid 100:106)A100 - 106
8X-RAY DIFFRACTION8(chain A and resid 107:125)A107 - 125
9X-RAY DIFFRACTION9(chain A and resid 126:133)A126 - 133
10X-RAY DIFFRACTION10(chain A and resid 134:149)A134 - 149
11X-RAY DIFFRACTION11(chain A and resid 150:153)A150 - 153
12X-RAY DIFFRACTION12(chain A and resid 154:167)A154 - 167
13X-RAY DIFFRACTION13(chain A and resid 168:192)A168 - 192
14X-RAY DIFFRACTION14(chain A and resid 193:198)A193 - 198
15X-RAY DIFFRACTION15(chain A and resid 199:205)A199 - 205
16X-RAY DIFFRACTION16(chain A and resid 206:215)A206 - 215
17X-RAY DIFFRACTION17(chain A and resid 216:219)A216 - 219
18X-RAY DIFFRACTION18(chain A and resid 220:224)A220 - 224
19X-RAY DIFFRACTION19(chain B and resid 4:13)B4 - 13
20X-RAY DIFFRACTION20(chain B and resid 14:22)B14 - 22
21X-RAY DIFFRACTION21(chain B and resid 23:34)B23 - 34
22X-RAY DIFFRACTION22(chain B and resid 35:57)B35 - 57
23X-RAY DIFFRACTION23(chain B and resid 58:62)B58 - 62
24X-RAY DIFFRACTION24(chain B and resid 63:74)B63 - 74
25X-RAY DIFFRACTION25(chain B and resid 75:79)B75 - 79
26X-RAY DIFFRACTION26(chain B and resid 80:123)B80 - 123
27X-RAY DIFFRACTION27(chain B and resid 124:128)B124 - 128
28X-RAY DIFFRACTION28(chain B and resid 129:134)B129 - 134
29X-RAY DIFFRACTION29(chain B and resid 135:148)B135 - 148
30X-RAY DIFFRACTION30(chain B and resid 149:158)B149 - 158
31X-RAY DIFFRACTION31(chain B and resid 159:167)B159 - 167
32X-RAY DIFFRACTION32(chain B and resid 168:184)B168 - 184
33X-RAY DIFFRACTION33(chain B and resid 185:199)B185 - 199
34X-RAY DIFFRACTION34(chain B and resid 200:205)B200 - 205
35X-RAY DIFFRACTION35(chain B and resid 206:218)B206 - 218
36X-RAY DIFFRACTION36(chain B and resid 219:223)B219 - 223

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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