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- PDB-2abm: Crystal Structure of Aquaporin Z Tetramer Reveals both Open and C... -

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Basic information

Entry
Database: PDB / ID: 2abm
TitleCrystal Structure of Aquaporin Z Tetramer Reveals both Open and Closed Water-conducting Channels
ComponentsAquaporin Z
KeywordsMEMBRANE PROTEIN / AQUAPORIN
Function / homology
Function and homology information


water channel activity / intracellular water homeostasis / water transport / response to osmotic stress / identical protein binding / plasma membrane
Similarity search - Function
Aquaporin Z / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / Chem-AGA / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / Chem-POQ / Aquaporin Z
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJiang, J. / Daniels, B.V. / Fu, D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of AqpZ Tetramer Reveals Two Distinct Arg-189 Conformations Associated with Water Permeation through the Narrowest Constriction of the Water-conducting Channel.
Authors: Jiang, J. / Daniels, B.V. / Fu, D.
History
DepositionJul 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 29, 2014Group: Non-polymer description
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Aug 23, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 1 .. 227 E 1 .. 227 0.162 M 1 B 1 .. 227 F 1 .. 227 0.170 M 1 C 1 .. 227 G 1 .. 227 0.156 M 1 D 1 .. 227 H 1 .. 227 0.158 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK:
Remark 600HETEROGEN ATOMS FOR SEVERAL LIGANDS WERE MISSING IN THE DENSITY. THE LIGANDS IN QUESTION ARE: BGL ...HETEROGEN ATOMS FOR SEVERAL LIGANDS WERE MISSING IN THE DENSITY. THE LIGANDS IN QUESTION ARE: BGL 604, 608, 605, 609. PEE 602, 606, 612, 613 AGA 629, 639. PEE 603, 607, 611.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,42028
Polymers189,7418
Non-polymers8,67920
Water9,710539
1
A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,45015
Polymers94,8714
Non-polymers4,57911
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16820 Å2
ΔGint-186 kcal/mol
Surface area27070 Å2
MethodPISA
2
E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,97113
Polymers94,8714
Non-polymers4,1009
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17450 Å2
ΔGint-200 kcal/mol
Surface area26710 Å2
MethodPISA
3
A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
hetero molecules

A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
hetero molecules

E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules

E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,84156
Polymers379,48316
Non-polymers17,35840
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation5_565-x,y+1,-z1
Buried area73490 Å2
ΔGint-794 kcal/mol
Surface area102610 Å2
MethodPISA
4
A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
hetero molecules

A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
hetero molecules

E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules

E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,84156
Polymers379,48316
Non-polymers17,35840
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation8_565-y,-x+1,-z+1/41
Buried area73250 Å2
ΔGint-795 kcal/mol
Surface area102860 Å2
MethodPISA
5
A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules

A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,84156
Polymers379,48316
Non-polymers17,35840
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area81580 Å2
ΔGint-848 kcal/mol
Surface area94520 Å2
MethodPISA
6
A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules

A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,84156
Polymers379,48316
Non-polymers17,35840
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area81410 Å2
ΔGint-847 kcal/mol
Surface area94690 Å2
MethodPISA
7
A: Aquaporin Z
B: Aquaporin Z
C: Aquaporin Z
D: Aquaporin Z
hetero molecules

E: Aquaporin Z
F: Aquaporin Z
G: Aquaporin Z
H: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,42028
Polymers189,7418
Non-polymers8,67920
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area35180 Å2
ΔGint-392 kcal/mol
Surface area52880 Å2
MethodPISA
8


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39140 Å2
ΔGint-419 kcal/mol
Surface area48920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.152, 119.152, 380.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.57467, 0.81768, -0.03404), (0.81778, -0.57535, -0.01457), (-0.0315, -0.01946, -0.99931)
Vector: 8.86685, -14.5761, 47.9516)
DetailsThe second tetramer (E,F,G,H) and the first tetramer (A,B,C,D) are related by a non-crystallographic 2-fold symmetry as rotation=( 0.57467 0.81768 -0.03404 ) ( 0.81778 -0.57535 -0.01457 ) ( -0.03150 -0.01946 -0.99931 ) translation=( 8.86685 -14.57612 47.95166 )

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEFGH

#1: Protein
Aquaporin Z / Bacterial nodulin-like intrinsic protein


Mass: 23717.662 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aqpZ, bniP / Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60844
#2: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 555 molecules

#3: Chemical ChemComp-POQ / BIS(((3S,4S,5R,6R)-5-(ETHYL(PHOSPHORYLOXY))-3,4,6-TRIHYDROXY-TETRAHYDRO-2H-PYRAN-2-YL)METHYL) HYDROGEN PHOSPHATE


Mass: 638.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H33O20P3
#4: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#7: Chemical ChemComp-AGA / (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE / PHOSPHATIDYL GLYCEROL


Mass: 455.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36O10P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 539 / 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 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 16% PEG3350, 0.75%beta-OG, 20% glycerol, 0.064 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorDetector: CCD / Date: May 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 46497 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.012 / Net I/σ(I): 9.8
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2239 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fx8

1fx8


Resolution: 3.2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 35679.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2143 5 %RANDOM
Rwork0.186 ---
all0.2 ---
obs0.186 43046 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.2004 Å2 / ksol: 0.353831 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.35 Å20 Å20 Å2
2--6.35 Å20 Å2
3----12.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-6 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13144 0 263 539 13946
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shellResolution: 3.2→3.39 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 309 4.6 %
Rwork0.287 6370 -
obs-6370 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4og.parog.top

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