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- PDB-3two: The crystal structure of CAD from Helicobacter pylori complexed w... -

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Basic information

Entry
Database: PDB / ID: 3two
TitleThe crystal structure of CAD from Helicobacter pylori complexed with NADP(H)
ComponentsMannitol dehydrogenase
KeywordsOXIDOREDUCTASE / Helicobacter pylori / Cinnamyl-alcohol dehydrogenase / NADP(H)
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Mannitol dehydrogenase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsSeo, K.H. / Zhuang, N.N. / Cong, C. / Lee, K.H.
CitationJournal: Febs Lett. / Year: 2012
Title: Unusual NADPH conformation in the crystal structure of a cinnamyl alcohol dehydrogenase from Helicobacter pylori in complex with NADP(H) and substrate docking analysis
Authors: Seo, K.H. / Zhuang, N.N. / Chen, C. / Song, J.Y. / Kang, H.L. / Rhee, K.H. / Lee, K.H.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Nov 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_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mannitol dehydrogenase
B: Mannitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2268
Polymers77,4732
Non-polymers1,7526
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-35 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.410, 85.680, 100.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PHEPHEAA1 - 3471 - 347
2ASPASPBB1 - 3481 - 348

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Components

#1: Protein Mannitol dehydrogenase / Cinnamyl-alcohol dehydrogenase


Mass: 38736.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 51 / Gene: cad / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosserta(DE3)pLysi / References: UniProt: D0ITF8, cinnamyl-alcohol dehydrogenase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Bis-Tris(pH6.5), 0.2M MgCl2, 19% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 38962 / % possible obs: 100 % / Observed criterion σ(I): 0.2 / Redundancy: 14.3 % / Rmerge(I) obs: 0.136
Reflection shellHighest resolution: 2.182 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 9.5 / Num. unique all: 10571 / Rsym value: 0.136 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQD

1yqd


Resolution: 2.18→43.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.881 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22593 1949 5 %RANDOM
Rwork0.17332 ---
obs0.17594 37013 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.012 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.094 Å0.023 Å
Luzzati d res low-0 Å
Luzzati sigma a0.231 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.18→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5437 0 100 45 5582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225678
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9827683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02724.506233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58215977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4381512
X-RAY DIFFRACTIONr_chiral_restr0.1960.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214208
X-RAY DIFFRACTIONr_mcbond_it0.861.53447
X-RAY DIFFRACTIONr_mcangle_it1.45625570
X-RAY DIFFRACTIONr_scbond_it2.80532231
X-RAY DIFFRACTIONr_scangle_it4.2494.52113
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2714 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.220.5
medium thermal0.962
LS refinement shellResolution: 2.182→2.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 148 -
Rwork0.171 2639 -
obs-1072 97.48 %
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)
10.5930.0406-0.1570.56720.2791.51640.02040.07430.043-0.0316-0.04440.0668-0.1107-0.16730.02410.02230.0219-0.00930.0299-0.0050.052433.93881.201939.9022
20.7002-0.06520.25740.49060.11670.9489-0.0319-0.07280.01160.06110.00450.03230.00680.0030.02740.0330.00020.00690.01-0.00370.009553.8094-4.220378.5167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 347
2X-RAY DIFFRACTION2B1 - 348

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