45IY | pdb_000045iy

Calcium-Coupled Proline Ring Puckering Defines a Structural Switch in a Thermophilic Lipase (Geobacillus kaustophilus)-Calcium-deficient

PDB DOI: https://doi.org/10.2210/pdb45IY/pdb

Classification: HYDROLASE
Organism(s): Geobacillus kaustophilus NBRC 102445
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-08-31 Released: 2026-09-16
Deposition Author(s): Eyerci, M.S., Tulek, A., Ozdemir, F.I., Sukur, G., DeMirci, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.210 (Depositor), 0.211 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Calcium-Coupled Proline Ring Puckering Defines a Structural Switch in a Thermophilic Lipase (Geobacillus kaustophilus)-Calcium-deficient

Eyerci, M.S., Tulek, A., Ozdemir, F.I., Sukur, G., DeMirci, H.

To be published.

Macromolecule Content

Total Structure Weight: 173.34 kDa
Atom Count: 12,282
Modeled Residue Count: 1,556
Deposited Residue Count: 1,556
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermoalkalophilic lipase	A, B, C, D	389	Geobacillus kaustophilus NBRC 102445	Mutation(s): 0 EC: 3.1.1.3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.210 (Depositor), 0.211 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.495	α = 89.965
b = 74.281	β = 89.984
c = 102.018	γ = 90.195

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
MrBUMP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Turkey	1919B012506377

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release