3BGE | pdb_00003bge

Crystal structure of the C-terminal fragment of AAA+ATPase from Haemophilus influenzae

PDB DOI: https://doi.org/10.2210/pdb3BGE/pdb

Classification: NUCLEOTIDE BINDING PROTEIN
Organism(s): Haemophilus influenzae 86-028NP
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-11-26 Released: 2008-01-01
Deposition Author(s): Ramagopal, U.A., Patskovsky, Y., Bonanno, J.B., Meyer, A.J., Toro, R., Freeman, J., Adams, J., Koss, J., Maletic, M., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.240 (Depositor), 0.238 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of the C-terminal fragment of AAA+ATPase from Haemophilus influenzae.

Ramagopal, U.A., Patskovsky, Y., Bonanno, J.B., Meyer, A.J., Toro, R., Freeman, J., Adams, J., Koss, J., Maletic, M., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 45.64 kDa
Atom Count: 2,855
Modeled Residue Count: 326
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted ATPase	A, B	201	Haemophilus influenzae 86-028NP	Mutation(s): 1 Gene Names: NTHI1458
UniProt
Find proteins for Q4QL22 (Haemophilus influenzae (strain 86-028NP)) Explore Q4QL22 Go to UniProtKB: Q4QL22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QL22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.240 (Depositor), 0.238 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.085	α = 90
b = 93.085	β = 90
c = 83.413	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-01-01

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-01-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2021-10-20
Changes: Database references
Version 1.6: 2023-08-30
Changes: Data collection, Refinement description