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- PDB-1mt5: CRYSTAL STRUCTURE OF FATTY ACID AMIDE HYDROLASE -

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Basic information

Entry
Database: PDB / ID: 1mt5
TitleCRYSTAL STRUCTURE OF FATTY ACID AMIDE HYDROLASE
ComponentsFatty-acid amide hydrolase
KeywordsHYDROLASE / AMIDASE SIGNATURE
Function / homology
Function and homology information


Arachidonic acid metabolism / fatty acid amide hydrolase / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / acylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / organelle membrane ...Arachidonic acid metabolism / fatty acid amide hydrolase / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / acylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / organelle membrane / positive regulation of vasoconstriction / fatty acid metabolic process / phospholipid binding / Golgi membrane / lipid binding / endoplasmic reticulum membrane / identical protein binding
Similarity search - Function
Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
METHYL ARACHIDONYL FLUOROPHOSPHONATE / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBracey, M.H. / Hanson, M.A. / Masuda, K.R. / Stevens, R.C. / Cravatt, B.F.
CitationJournal: science / Year: 2002
Title: Structural Adaptations in a Membrane Enzyme That Terminates Endocannabinoid Signaling
Authors: Bracey, M.H. / Hanson, M.A. / Masuda, K.R. / Stevens, R.C. / Cravatt, B.F.
History
DepositionSep 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty-acid amide hydrolase
B: Fatty-acid amide hydrolase
C: Fatty-acid amide hydrolase
D: Fatty-acid amide hydrolase
E: Fatty-acid amide hydrolase
F: Fatty-acid amide hydrolase
G: Fatty-acid amide hydrolase
H: Fatty-acid amide hydrolase
I: Fatty-acid amide hydrolase
J: Fatty-acid amide hydrolase
K: Fatty-acid amide hydrolase
L: Fatty-acid amide hydrolase
M: Fatty-acid amide hydrolase
N: Fatty-acid amide hydrolase
O: Fatty-acid amide hydrolase
P: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)949,01632
Polymers943,08816
Non-polymers5,92816
Water0
1
A: Fatty-acid amide hydrolase
B: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-21 kcal/mol
Surface area34810 Å2
MethodPISA
2
C: Fatty-acid amide hydrolase
D: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-21 kcal/mol
Surface area34750 Å2
MethodPISA
3
E: Fatty-acid amide hydrolase
F: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-22 kcal/mol
Surface area34600 Å2
MethodPISA
4
G: Fatty-acid amide hydrolase
H: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-21 kcal/mol
Surface area34910 Å2
MethodPISA
5
I: Fatty-acid amide hydrolase
J: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-20 kcal/mol
Surface area34770 Å2
MethodPISA
6
K: Fatty-acid amide hydrolase
L: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-22 kcal/mol
Surface area34790 Å2
MethodPISA
7
M: Fatty-acid amide hydrolase
N: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-20 kcal/mol
Surface area34920 Å2
MethodPISA
8
O: Fatty-acid amide hydrolase
P: Fatty-acid amide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6274
Polymers117,8862
Non-polymers7412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-23 kcal/mol
Surface area34770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.107, 272.019, 147.216
Angle α, β, γ (deg.)90.00, 115.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171A
181B
191C
201D
211E
221F
231G
241H
251I
261J
271K
281L
291M
301N
311O
321P

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALATHR5AA37 - 5731 - 537
21ALATHR5BB37 - 5731 - 537
31ALATHR5CC37 - 5731 - 537
41ALATHR5DD37 - 5731 - 537
51ALATHR5EE37 - 5731 - 537
61ALATHR5FF37 - 5731 - 537
71ALATHR5GG37 - 5731 - 537
81ALATHR5HH37 - 5731 - 537
91ALATHR5II37 - 5731 - 537
101ALATHR5JJ37 - 5731 - 537
111ALATHR5KK37 - 5731 - 537
121ALATHR5LL37 - 5731 - 537
131ALATHR5MM37 - 5731 - 537
141ALATHR5NN37 - 5731 - 537
151ALATHR5OO37 - 5731 - 537
161ALATHR5PP37 - 5731 - 537
172MAYMAY1AQ600
182MAYMAY1BR600
192MAYMAY1CS600
202MAYMAY1DT600
212MAYMAY1EU600
222MAYMAY1FV600
232MAYMAY1GW600
242MAYMAY1HX600
252MAYMAY1IY600
262MAYMAY1JZ600
272MAYMAY1KAA600
282MAYMAY1LBA600
292MAYMAY1MCA600
302MAYMAY1NDA600
312MAYMAY1OEA600
322MAYMAY1PFA600

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Components

#1: Protein
Fatty-acid amide hydrolase / Oleamide hydrolase / Anandamide amidohydrolase


Mass: 58943.031 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FAAH / Plasmid: pTrcHis / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P97612, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MAY / METHYL ARACHIDONYL FLUOROPHOSPHONATE / MAFP / Methoxy arachidonyl fluorophosphonate


Mass: 370.482 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H36FO2P / Comment: inhibitor*YM

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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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, 2,4-methyl pentanediol, sodium citrate, lithium sulphate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
2100 mMsodium citrate1reservoirpH5.
3100 mMlithium sulfate1reservoir
47 %(w/v)PEG60001reservoir
55 %(v/v)MPD1reservoir
60-20 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 243192 / Num. obs: 173615 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.104 / Net I/σ(I): 4.4
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 76 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 79 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAAH structure in an alternate spacegroup. Solved by MAD/MIRAS phasing.

Resolution: 2.8→141.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 19.283 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.51
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Refinemant carried out while the manuscript was in press resulted in improved geometry at the cost of slightly higher R values. Atoms for which no density was observed were not included in ...Details: Refinemant carried out while the manuscript was in press resulted in improved geometry at the cost of slightly higher R values. Atoms for which no density was observed were not included in the refinement. Refinement was performed by first detwinning the data using the molecular model. Followed by rounds of refinement and rebuilding and additional iterations of the detwinning procedure. No sigma cutoff was used due to details of the detwinning. The final Rtwin = 0.272
RfactorNum. reflection% reflectionSelection details
Rfree0.26228 9297 5.1 %RANDOM
Rwork0.2184 ---
obs0.22062 173616 71.37 %-
all-243192 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.594 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-0.94 Å2
2--4.38 Å20 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64140 0 384 0 64524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02265996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.98489778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.73658576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.210320
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0249656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1260.331512
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.52787
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.371
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.952242832
X-RAY DIFFRACTIONr_mcangle_it1.671368512
X-RAY DIFFRACTIONr_scbond_it0.911223164
X-RAY DIFFRACTIONr_scangle_it1.422321266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A24tight positional0.040.05
2B24tight positional0.060.05
3C24tight positional0.040.05
4D24tight positional0.070.05
5E24tight positional0.060.05
6F24tight positional0.060.05
7G24tight positional0.050.05
8H24tight positional0.060.05
9I24tight positional0.050.05
10J24tight positional0.050.05
11K24tight positional0.050.05
12L24tight positional0.050.05
13M24tight positional0.060.05
14N24tight positional0.050.05
15O24tight positional0.050.05
16P24tight positional0.060.05
1A4008medium positional0.30.5
2B4008medium positional0.30.5
3C4008medium positional0.290.5
4D4008medium positional0.280.5
5E4008medium positional0.320.5
6F4008medium positional0.310.5
7G4008medium positional0.290.5
8H4008medium positional0.30.5
9I4008medium positional0.280.5
10J4008medium positional0.30.5
11K4008medium positional0.30.5
12L4008medium positional0.30.5
13M4008medium positional0.460.5
14N4008medium positional0.340.5
15O4008medium positional0.290.5
16P4008medium positional0.310.5
1A24tight thermal0.080.5
2B24tight thermal0.080.5
3C24tight thermal0.090.5
4D24tight thermal0.070.5
5E24tight thermal0.080.5
6F24tight thermal0.070.5
7G24tight thermal0.070.5
8H24tight thermal0.10.5
9I24tight thermal0.10.5
10J24tight thermal0.070.5
11K24tight thermal0.110.5
12L24tight thermal0.090.5
13M24tight thermal0.170.5
14N24tight thermal0.180.5
15O24tight thermal0.090.5
16P24tight thermal0.070.5
1A4008medium thermal0.842
2B4008medium thermal0.672
3C4008medium thermal0.922
4D4008medium thermal0.922
5E4008medium thermal0.662
6F4008medium thermal0.782
7G4008medium thermal0.722
8H4008medium thermal0.892
9I4008medium thermal0.652
10J4008medium thermal0.672
11K4008medium thermal0.632
12L4008medium thermal0.692
13M4008medium thermal1.422
14N4008medium thermal1.222
15O4008medium thermal0.622
16P4008medium thermal0.752
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 728
Rwork0.279 12811
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. reflection obs: 173615 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.029
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.041

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