1PMH

Crystal structure of Caldicellulosiruptor saccharolyticus CBM27-1 in complex with mannohexaose

• PDB DOI: https://doi.org/10.2210/pdb1PMH/pdb

• Classification: HYDROLASE
• Organism(s): Caldicellulosiruptor saccharolyticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-06-11 Released: 2004-06-22 
• Deposition Author(s): Roske, Y., Sunna, A., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.173 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.18 kDa 
• Atom Count: 1,904 
• Modelled Residue Count: 183 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-1,4-mannanase	A [auth X]	185	Caldicellulosiruptor saccharolyticus	Mutation(s): 2  Gene Names: manA EC: 3.2.1.78
UniProt
Find proteins for P77847 (Caldicellulosiruptor saccharolyticus) Explore P77847  Go to UniProtKB:  P77847

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	B [auth A]	6		N/A
Glycosylation Resources
GlyTouCan:  G39448BE GlyCosmos:  G39448BE GlyGen:  G39448BE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth X], E [auth X], F [auth X], G [auth X]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.173 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.281	α = 90
b = 45.7	β = 90
c = 110.113	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-22 
Deposition Author(s): Roske, Y., Sunna, A., Heinemann, U.

Revision History  

• Version 1.0: 2004-06-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary