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- PDB-5ayj: Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C -

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Basic information

Entry
Database: PDB / ID: 5ayj
TitleHyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C
ComponentsUric acid degradation bifunctional protein
KeywordsOXIDOREDUCTASE / Disulfide bond / Thermostability / Protein engineering / Oxidase / Subunit-subunit interaction
Function / homology
Function and homology information


2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / allantoin metabolic process / purine nucleobase metabolic process
Similarity search - Function
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily / OHCU decarboxylase / Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase ...2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily / OHCU decarboxylase / Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
9-METHYL URIC ACID / Uric acid degradation bifunctional protein
Similarity search - Component
Biological speciesBacillus sp. TB-90 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHibi, T. / Kume, A. / Kawamura, A. / Itoh, T. / Nishiya, Y.
Citation
Journal: Biochemistry / Year: 2016
Title: Hyperstabilization of Tetrameric Bacillus sp. TB-90 Urate Oxidase by Introducing Disulfide Bonds through Structural Plasticity
Authors: Hibi, T. / Kume, A. / Kawamura, A. / Itoh, T. / Fukada, H. / Nishiya, Y.
#1: Journal: Biochemistry / Year: 2014
Title: Intersubunit salt bridges with a sulfate anion control subunit dissociation and thermal stabilization of Bacillus sp. TB-90 urate oxidase.
Authors: Hibi, T. / Hayashi, Y. / Fukada, H. / Itoh, T. / Nago, T. / Nishiya, Y.
History
DepositionAug 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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: Uric acid degradation bifunctional protein
B: Uric acid degradation bifunctional protein
C: Uric acid degradation bifunctional protein
D: Uric acid degradation bifunctional protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,22918
Polymers151,4224
Non-polymers2,80714
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25920 Å2
ΔGint-121 kcal/mol
Surface area40840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.861, 142.581, 70.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-512-

HOH

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Components

#1: Protein
Uric acid degradation bifunctional protein / Urate oxidase


Mass: 37855.594 Da / Num. of mol.: 4 / Fragment: UNP residues 172-502 / Mutation: R298C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. TB-90 (bacteria) / Strain: TB-90 / Gene: uao / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q45697, factor-independent urate hydroxylase
#2: Chemical
ChemComp-MUA / 9-METHYL URIC ACID


Mass: 182.137 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6N4O3
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.18 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% (w/v) polyethylene glycol 8000, 100mM Tris-HCl pH 8.0, 0.08M Li2SO4, 1mM 9-methyluric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 83842 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 20.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WLV
Resolution: 2.05→32.269 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 4245 5.07 %
Rwork0.1694 --
obs0.172 83730 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→32.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9297 0 125 429 9851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099632
X-RAY DIFFRACTIONf_angle_d1.1513070
X-RAY DIFFRACTIONf_dihedral_angle_d12.1763375
X-RAY DIFFRACTIONf_chiral_restr0.0471476
X-RAY DIFFRACTIONf_plane_restr0.0061642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.30351370.24692275X-RAY DIFFRACTION87
2.0733-2.09760.27531510.21282621X-RAY DIFFRACTION100
2.0976-2.12320.26011350.19752629X-RAY DIFFRACTION100
2.1232-2.15010.24481370.18862635X-RAY DIFFRACTION100
2.1501-2.17840.23421310.18222647X-RAY DIFFRACTION100
2.1784-2.20820.27021310.17292658X-RAY DIFFRACTION100
2.2082-2.23970.24691520.18622603X-RAY DIFFRACTION100
2.2397-2.27320.21981370.20782655X-RAY DIFFRACTION100
2.2732-2.30870.25361200.17252641X-RAY DIFFRACTION100
2.3087-2.34650.22071350.16382648X-RAY DIFFRACTION100
2.3465-2.3870.21281270.15672632X-RAY DIFFRACTION100
2.387-2.43040.20951550.1592640X-RAY DIFFRACTION100
2.4304-2.47710.21771590.16472627X-RAY DIFFRACTION100
2.4771-2.52760.23621400.16452671X-RAY DIFFRACTION100
2.5276-2.58260.2181660.162606X-RAY DIFFRACTION100
2.5826-2.64260.20781180.16352661X-RAY DIFFRACTION100
2.6426-2.70870.22521470.1552646X-RAY DIFFRACTION100
2.7087-2.78190.22481690.15682613X-RAY DIFFRACTION100
2.7819-2.86370.22171460.15752652X-RAY DIFFRACTION100
2.8637-2.95610.21881290.1562685X-RAY DIFFRACTION100
2.9561-3.06160.17771340.14982673X-RAY DIFFRACTION100
3.0616-3.18410.20451610.17152649X-RAY DIFFRACTION100
3.1841-3.32890.21921350.16522678X-RAY DIFFRACTION100
3.3289-3.50420.22811400.16472667X-RAY DIFFRACTION100
3.5042-3.72340.20071480.15762688X-RAY DIFFRACTION100
3.7234-4.01040.22771360.16092682X-RAY DIFFRACTION100
4.0104-4.41310.1941240.14852758X-RAY DIFFRACTION100
4.4131-5.04960.1651280.14992718X-RAY DIFFRACTION100
5.0496-6.3540.27181420.19942724X-RAY DIFFRACTION99
6.354-32.27330.23631750.20412803X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.90310.11740.25450.2128-0.19510.7193-0.02970.0572-0.2886-0.1106-0.0335-0.12610.2533-0.17290.08980.241-0.0410.03910.1961-0.01420.278-16.465820.353279.0076
20.51730.4027-0.13833.4271-0.47941.0709-0.06210.1087-0.031-0.21890.08490.2270.1355-0.1051-0.01730.1542-0.0326-0.01430.2197-0.02090.1629-25.37333.019975.3676
32.6615-0.65733.13030.0848-1.24686.65960.0572-0.0189-0.0837-0.1388-0.05160.07640.4457-0.04530.07050.2254-0.0135-0.02220.115-0.06540.2187-14.288620.939381.6262
42.77460.1487-0.51520.4049-0.11560.0126-0.06350.1662-0.2531-0.0570.029-0.03330.08840.020.03640.25690.0319-0.01520.2545-0.04590.20685.641225.513869.1636
55.40293.58710.4182.47780.30680.7450.20780.1036-0.24420.3192-0.1306-0.27880.20310.132-0.05650.27340.0528-0.01990.2419-0.00680.19978.955123.790771.9396
64.70410.6726-0.77020.8216-0.19391.0947-0.16460.3719-0.4582-0.07710.1553-0.01830.2795-0.03240.02570.30990.0087-0.00940.1934-0.0650.2597-2.354614.321468.8553
77.34943.04764.64693.47671.30263.6157-0.25660.3411-0.151-0.23120.1165-0.0993-0.12320.3920.15640.24490.0210.07470.2728-0.0410.15624.613222.68571.9559
83.6574-0.08043.0413.45080.4185.2744-0.05130.1716-0.2045-0.08070.0644-0.22090.09410.22190.01560.16950.01290.06650.17360.00890.162611.413526.410674.8191
90.7268-1.14710.13881.95640.14370.5891-0.07850.0659-0.03330.06340.01850.09780.04810.03780.07870.1461-0.01130.02330.16650.0090.15726.874355.646573.0203
102.3180.43210.17354.73363.20953.0128-0.06220.3963-0.2186-0.2225-0.13660.08910.128-0.10920.15990.25240.01540.0290.27630.02050.160910.972433.477563.2324
112.4577-0.5589-0.17955.45781.72881.0345-0.09010.09210.0277-0.25030.1306-0.22380.0070.1632-0.03180.16810.02520.00860.22290.01630.133212.294345.624664.5119
125.17096.37746.59072.17341.94372.2209-0.1869-0.21430.4509-0.3105-0.31510.2554-0.3397-0.19450.42450.23520.00230.03610.2031-0.01090.310.378564.556390.2184
130.67440.1411.39031.78041.57557.08780.04680.19810.0226-0.0788-0.0015-0.10670.23850.1449-0.05960.11760.0380.01970.15040.02440.13695.715250.271170.9795
140.22020.0990.06810.597-0.19360.23660.01950.06650.00390.01370.01150.05940.0592-0.07070.00480.1496-0.0036-0.00530.1997-0.00220.1648-17.630149.434178.136
154.20030.8586-2.41631.7095-0.26532.20580.13140.10650.2561-0.10050.0764-0.0694-0.107-0.0142-0.17770.12850.0339-0.02080.1340.02560.1472-7.514360.676871.4904
168.96268.0928-5.49932.235-5.0425.03220.00920.34980.2976-0.19730.31670.4619-0.2025-0.4785-0.25430.18040.05090.01460.1761-0.00070.1915-17.911758.381871.8835
171.72271.9893-1.60752.6382-1.58782.80960.01440.03060.05350.01630.05460.18240.2289-0.2233-0.14190.08830.012-0.03030.22340.0150.2004-16.677451.68583.111
183.0340.908-0.86945.3759-5.14667.8257-0.00330.12630.3075-0.37240.0361-0.01390.4157-0.3625-0.03240.18420.0059-0.01530.1407-0.0330.2303-17.800247.623974.7338
190.58060.91990.01011.6938-0.15920.29-0.0565-0.04260.0775-0.08220.032-0.08750.0037-0.03970.04030.1720.01210.01580.1941-0.0010.2294-7.739855.8964103.7603
201.85050.0020.11355.9591-4.52964.4506-0.0253-0.2519-0.18090.1307-0.1193-0.15780.14650.17510.16820.2008-0.01390.00710.2486-0.03130.1342-13.138234.1614113.475
212.16680.42920.09274.4528-1.19471.1963-0.0057-0.2103-0.02190.14290.02370.15430.0372-0.1353-0.02440.1614-0.01920.00420.2459-0.00720.1616-13.801546.4192112.1267
223.7199-6.03155.24122.01471.71462.011-0.13070.09730.4907-0.0504-0.4665-0.5871-0.29940.26970.24830.1619-0.03370.02960.18240.02390.2584-10.804865.1586.4887
230.9903-0.26171.11071.446-2.12388.1010.1266-0.1621-0.0266-0.01710.02770.17660.3309-0.0177-0.12470.1122-0.0484-0.00780.1151-0.04040.147-6.997950.6519105.7365
240.55490.04750.18340.71740.00690.20490.00770.0692-0.0257-0.0837-0.0052-0.07070.07820.02460.02480.17850.0254-0.00530.1849-0.00330.171416.291348.506898.5821
255.0234-1.0524-2.37411.3960.12692.17550.0879-0.22740.25680.15190.01760.0426-0.12880.0466-0.13450.149-0.026-0.02050.1304-0.03140.16096.744460.3086105.4176
266.3482-6.2941-4.35328.33533.72474.38530.0056-0.22870.14030.15720.169-0.3949-0.09190.3117-0.23260.1352-0.0058-0.01550.2143-0.01440.162317.053557.4015104.8059
272.058-1.1647-2.03872.25532.39895.86790.06490.05570.0491-0.10620.0321-0.14110.03980.1435-0.09640.07690.0226-0.02040.1745-0.01550.183215.276251.291295.104
281.3359-0.731-1.30691.36370.02443.178-0.0855-0.16510.00750.1770.1162-0.11520.10380.3618-0.08310.16290.0349-0.06350.2449-0.0020.239116.763846.959498.5351
291.47450.5936-0.0170.9278-0.04240.3708-0.0446-0.1278-0.34150.0046-0.0632-0.00660.21060.10310.09970.30230.06870.01160.23280.02650.294413.564319.561897.904
300.57830.08180.08733.23250.72380.5613-0.0651-0.0225-0.05210.19490.0794-0.09670.11390.1314-0.02010.17460.0528-0.00860.230.02520.178523.16731.716101.3721
312.02680.92292.05050.44470.72393.58520.1167-0.1245-0.20740.05720.0383-0.13020.3162-0.0478-0.10790.22130.0211-0.02170.15680.04120.243711.99821.507998.6298
322.1947-1.8589-0.94971.55990.69230.4201-0.07060.1929-0.1480.0552-0.05660.19920.0906-0.1510.10380.2563-0.0645-00.30510.02120.2372-14.965425.4979105.5563
334.2329-0.97520.26551.4205-0.1981.11580.0569-0.2024-0.21470.1169-0.06620.04270.2611-0.02470.00060.2871-0.02450.00720.21440.03350.2044-3.047516.9274106.8621
343.95880.1984.49873.3289-0.81876.7462-0.0985-0.1547-0.23510.0960.04850.307-0.1586-0.09640.05680.10250.05960.09750.2029-0.01620.1815-14.07927.4063101.6485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 263 )
7X-RAY DIFFRACTION7chain 'A' and (resid 264 through 283 )
8X-RAY DIFFRACTION8chain 'A' and (resid 284 through 310 )
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 43 )
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 119 )
12X-RAY DIFFRACTION12chain 'B' and (resid 120 through 135 )
13X-RAY DIFFRACTION13chain 'B' and (resid 136 through 161 )
14X-RAY DIFFRACTION14chain 'B' and (resid 162 through 213 )
15X-RAY DIFFRACTION15chain 'B' and (resid 214 through 248 )
16X-RAY DIFFRACTION16chain 'B' and (resid 249 through 263 )
17X-RAY DIFFRACTION17chain 'B' and (resid 264 through 295 )
18X-RAY DIFFRACTION18chain 'B' and (resid 296 through 314 )
19X-RAY DIFFRACTION19chain 'C' and (resid 8 through 43 )
20X-RAY DIFFRACTION20chain 'C' and (resid 44 through 72 )
21X-RAY DIFFRACTION21chain 'C' and (resid 73 through 119 )
22X-RAY DIFFRACTION22chain 'C' and (resid 120 through 135 )
23X-RAY DIFFRACTION23chain 'C' and (resid 136 through 161 )
24X-RAY DIFFRACTION24chain 'C' and (resid 162 through 213 )
25X-RAY DIFFRACTION25chain 'C' and (resid 214 through 248 )
26X-RAY DIFFRACTION26chain 'C' and (resid 249 through 263 )
27X-RAY DIFFRACTION27chain 'C' and (resid 264 through 292 )
28X-RAY DIFFRACTION28chain 'C' and (resid 293 through 314 )
29X-RAY DIFFRACTION29chain 'D' and (resid 7 through 43 )
30X-RAY DIFFRACTION30chain 'D' and (resid 44 through 119 )
31X-RAY DIFFRACTION31chain 'D' and (resid 120 through 172 )
32X-RAY DIFFRACTION32chain 'D' and (resid 173 through 213 )
33X-RAY DIFFRACTION33chain 'D' and (resid 214 through 283 )
34X-RAY DIFFRACTION34chain 'D' and (resid 284 through 310 )

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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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