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- PDB-2z0b: Crystal structure of CBM20 domain of human putative glycerophosph... -

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Basic information

Entry
Database: PDB / ID: 2z0b
TitleCrystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)
ComponentsPutative glycerophosphodiester phosphodiesterase 5
KeywordsHYDROLASE / GDE5 / KIAA1434 / CBM20 domain / starch-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


glycerophosphocholine phosphodiesterase / Hydrolysis of LPE / glycerophosphocholine phosphodiesterase activity / glycerophospholipid catabolic process / Hydrolysis of LPC / starch binding / skeletal muscle tissue development / cytosol
Similarity search - Function
Glycerophosphocholine phosphodiesterase GPCPD1, CBM20 domain / Glycerophosphodiester phosphodiesterase Gde1 / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold ...Glycerophosphocholine phosphodiesterase GPCPD1, CBM20 domain / Glycerophosphodiester phosphodiesterase Gde1 / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Glycerophosphocholine phosphodiesterase GPCPD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSaijo, S. / Nishino, A. / Kishishita, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)
Authors: Saijo, S. / Nishino, A. / Kishishita, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative glycerophosphodiester phosphodiesterase 5
B: Putative glycerophosphodiester phosphodiesterase 5
C: Putative glycerophosphodiester phosphodiesterase 5
D: Putative glycerophosphodiester phosphodiesterase 5
E: Putative glycerophosphodiester phosphodiesterase 5
F: Putative glycerophosphodiester phosphodiesterase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5658
Polymers84,3756
Non-polymers1902
Water8,071448
1
A: Putative glycerophosphodiester phosphodiesterase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1582
Polymers14,0631
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative glycerophosphodiester phosphodiesterase 5


Theoretical massNumber of molelcules
Total (without water)14,0631
Polymers14,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative glycerophosphodiester phosphodiesterase 5


Theoretical massNumber of molelcules
Total (without water)14,0631
Polymers14,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative glycerophosphodiester phosphodiesterase 5


Theoretical massNumber of molelcules
Total (without water)14,0631
Polymers14,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative glycerophosphodiester phosphodiesterase 5


Theoretical massNumber of molelcules
Total (without water)14,0631
Polymers14,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative glycerophosphodiester phosphodiesterase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1582
Polymers14,0631
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Putative glycerophosphodiester phosphodiesterase 5
F: Putative glycerophosphodiester phosphodiesterase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3154
Polymers28,1252
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-25 kcal/mol
Surface area11960 Å2
MethodPISA
8
B: Putative glycerophosphodiester phosphodiesterase 5
C: Putative glycerophosphodiester phosphodiesterase 5


Theoretical massNumber of molelcules
Total (without water)28,1252
Polymers28,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10.2 kcal/mol
Surface area11610 Å2
MethodPISA
9
D: Putative glycerophosphodiester phosphodiesterase 5
E: Putative glycerophosphodiester phosphodiesterase 5


Theoretical massNumber of molelcules
Total (without water)28,1252
Polymers28,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-10.7 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.040, 111.040, 77.385
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Putative glycerophosphodiester phosphodiesterase 5 / / GDE5 / KIAA1434


Mass: 14062.577 Da / Num. of mol.: 6 / Fragment: CBM20 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDE5, KIAA1434 / Plasmid: PK051017-07 / Production host: Cell-free protein synthesis
References: UniProt: Q9NPB8, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.0M Sodium/Potassium Phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979270, 0.979740, 0.96400
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 22, 2006 / Details: rhodium coated mirror
RadiationMonochromator: fixed exit double crystal monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979741
30.9641
ReflectionResolution: 2→50 Å / Num. obs: 65368 / % possible obs: 90.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.052 / Net I/σ(I): 29.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1809 / Rsym value: 0.287 / % possible all: 50.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.127 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The structure was refined also with CNS 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3302 5.1 %RANDOM
Rwork0.221 ---
obs0.222 62030 90.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 10 448 5590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225308
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9557220
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1695659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83324.336226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57815847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2161525
X-RAY DIFFRACTIONr_chiral_restr0.080.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024007
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.22176
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23514
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2461
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.53407
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8825334
X-RAY DIFFRACTIONr_scbond_it1.04932222
X-RAY DIFFRACTIONr_scangle_it1.5684.51880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 162 -
Rwork0.253 2582 -
obs-2744 51.19 %
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)
11.6963-1.80791.25334.7796-2.32745.24080.0761-0.0925-0.08350.03590.16730.19080.31680.2957-0.24340.10190.05390.01820.03830.0068-0.102542.40357.1114.095
25.9578-1.31941.34724.77490.67854.08490.08550.1493-0.3894-0.1337-0.13211.14960.3371-0.50280.04660.0137-0.073-0.0859-0.0516-0.02190.112426.90148.363-25.299
32.6515-0.34911.01361.5498-0.15244.672-0.04290.00880.1437-0.03590.05280.0292-0.32990.3049-0.00990.1115-0.05620.02440.0829-0.0046-0.124856.37137.335-13.524
42.3070.3645-1.04261.7369-0.36065.1356-0.0641-0.0056-0.13460.02710.06280.0410.3580.32260.00130.09560.0551-0.02180.0744-0.0057-0.137156.50390.646-10.688
57.12171.5249-1.37955.85210.80734.20590.0936-0.10270.44120.212-0.11711.2119-0.3998-0.50180.02350.03020.07230.099-0.0662-0.0180.088527.12380.2020.991
61.47411.6934-1.02224.5053-2.49815.10560.06820.0720.0882-0.01520.16510.1833-0.29680.3071-0.23330.1035-0.0542-0.01550.04170.0091-0.101942.32270.994-28.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1206 - 120
2X-RAY DIFFRACTION2BB6 - 1186 - 118
3X-RAY DIFFRACTION3CC1 - 1211 - 121
4X-RAY DIFFRACTION4DD4 - 1204 - 120
5X-RAY DIFFRACTION5EE8 - 1198 - 119
6X-RAY DIFFRACTION6FF8 - 1188 - 118

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