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- PDB-1pmh: Crystal structure of Caldicellulosiruptor saccharolyticus CBM27-1... -

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Basic information

Entry
Database: PDB / ID: 1pmh
TitleCrystal structure of Caldicellulosiruptor saccharolyticus CBM27-1 in complex with mannohexaose
Componentsbeta-1,4-mannanase
KeywordsHYDROLASE / jellyroll beta-sandwich
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / carbohydrate binding / metal ion binding
Similarity search - Function
Carbohydrate binding module 27 / Carbohydrate binding module 27 / Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding domain-like ...Carbohydrate binding module 27 / Carbohydrate binding module 27 / Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Beta-1,4-mannanase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.06 Å
AuthorsRoske, Y. / Sunna, A. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose.
Authors: Roske, Y. / Sunna, A. / Pfeil, W. / Heinemann, U.
History
DepositionJun 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE According to the author there is a mistake in the sequence database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1827
Polymers20,9031
Non-polymers1,2796
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.281, 45.700, 110.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein beta-1,4-mannanase / CsCBM27-1


Mass: 20903.033 Da / Num. of mol.: 1 / Fragment: Carbohydrate binding module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria)
Strain: Rt8B.4 / Gene: manA / Plasmid: pPROEX HTc / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: GenBank: 1491795, UniProt: P77847*PLUS, mannan endo-1,4-beta-mannosidase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a1122h-1a_1-5][a1122h-1b_1-5]/1-2-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, Isopropanol, Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.9795
SYNCHROTRONBESSY 14.220.97981
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEJan 30, 2003mirrors
MARRESEARCH2IMAGE PLATEJan 30, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979811
ReflectionResolution: 1.06→30 Å / Num. all: 84822 / Num. obs: 81658 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 8.8 Å2 / Rsym value: 0.048 / Net I/σ(I): 34.6
Reflection shellResolution: 1.06→1.09 Å / Num. unique all: 1544 / Rsym value: 0.09 / % possible all: 74.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.06→23 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.469 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1729 4226 5 %RANDOM
Rwork0.14132 ---
all0.204 84822 --
obs0.14287 80596 95.9 %-
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: 17.624 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2---0.74 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.06→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 97 279 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221662
X-RAY DIFFRACTIONr_bond_other_d0.0010.021430
X-RAY DIFFRACTIONr_angle_refined_deg2.072.0052250
X-RAY DIFFRACTIONr_angle_other_deg1.80133360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3535182
X-RAY DIFFRACTIONr_chiral_restr0.1330.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021727
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02319
X-RAY DIFFRACTIONr_nbd_refined0.2350.2295
X-RAY DIFFRACTIONr_nbd_other0.2670.21618
X-RAY DIFFRACTIONr_nbtor_other0.0930.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3540.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.240
X-RAY DIFFRACTIONr_mcbond_it2.9483918
X-RAY DIFFRACTIONr_mcangle_it3.94561500
X-RAY DIFFRACTIONr_scbond_it5.3285744
X-RAY DIFFRACTIONr_scangle_it6.7797.5750
X-RAY DIFFRACTIONr_rigid_bond_restr2.7752.51662
X-RAY DIFFRACTIONr_sphericity_free15.474283
X-RAY DIFFRACTIONr_sphericity_bonded9.37541624
LS refinement shellResolution: 1.06→1.087 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 255 -
Rwork0.394 5099 -
obs-71983 82.5 %

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