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- PDB-1gmg: ALANINE 31 PROLINE MUTANT OF ROP PROTEIN, MONOCLINIC FORM -

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Basic information

Entry
Database: PDB / ID: 1gmg
TitleALANINE 31 PROLINE MUTANT OF ROP PROTEIN, MONOCLINIC FORM
ComponentsREGULATORY PROTEIN ROP
KeywordsTRANSCRIPTION REGULATION
Function / homologyHelix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGlykos, N.M. / Kokkinidis, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure Determination of a Small Protein Through a 23-Dimensional Molecular-Replacement Search.
Authors: Glykos, N.M. / Kokkinidis, M.
#1: Journal: Structure / Year: 1999
Title: Protein Plasticity to the Extreme: Changing the Topology of a 4-Alpha-Helical Bundle with a Single Amino-Acid Substitution
Authors: Glykos, N.M. / Cesareni, G. / Kokkinidis, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Meaningful Refinement of Poly-Alanine Models Using Rigid-Body Simulated Annealing : Application to the Structure Determination of the A31P Rop Mutant
Authors: Glykos, N.M. / Kokkinidis, M.
History
DepositionSep 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATORY PROTEIN ROP
B: REGULATORY PROTEIN ROP


Theoretical massNumber of molelcules
Total (without water)14,5262
Polymers14,5262
Non-polymers00
Water1,65792
1
A: REGULATORY PROTEIN ROP

A: REGULATORY PROTEIN ROP


Theoretical massNumber of molelcules
Total (without water)14,5262
Polymers14,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
2
B: REGULATORY PROTEIN ROP

B: REGULATORY PROTEIN ROP


Theoretical massNumber of molelcules
Total (without water)14,5262
Polymers14,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)94.390, 24.250, 64.530
Angle α, β, γ (deg.)90.00, 130.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

21A-2046-

HOH

31B-2035-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99579, 0.02097, 0.0892), (-0.01906, -0.99957, 0.02217), (0.08963, 0.02038, 0.99577)
Vector: -23.32356, 28.6406, -23.16492)
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWOCRYSTALLOGRAPHICALLY INDEPENDENT MONOMERS (HALF BUNDLES).THE TWO COMPLETE 4-ALPHA-HELICAL BUNDLES ARE FORMED THROUGHTHE APPLICATION OF CRYSTALLOGRAPHIC SYMMETRY OPERATORSCORRESPONDING TO THE TWO-FOLD AXES (PARALLEL TO Y) ATX=0.00, Z= 0.00 AND AT X=0.50, Z=0.50.THE CHAIN IN THE COMPLEX ARE 1268.5 ANGSTROM**2AND 1158. 3 ANGSTROM**2

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Components

#1: Protein REGULATORY PROTEIN ROP / RNA ONE MODULATOR / ROM


Mass: 7263.076 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: 71/72 (71/18 PLUS PCI857)URCE 8 / Plasmid: PEX43 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION ALA31PRO

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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: 2.13 Å3/Da / Density % sol: 41.8 %
Description: THE STRUCTURE WAS DETERMINED THROUGH A 23-DIMENSIONAL MOLECULAR REPLACEMENT SEARCH PERFORMED WITH THE PROGRAM QUEEN OF SPADES AND USING AS A SEARCH MODEL ONE POLY-ALANINE HELIX ...Description: THE STRUCTURE WAS DETERMINED THROUGH A 23-DIMENSIONAL MOLECULAR REPLACEMENT SEARCH PERFORMED WITH THE PROGRAM QUEEN OF SPADES AND USING AS A SEARCH MODEL ONE POLY-ALANINE HELIX ACCOUNTING FOR 13% OF THE TOTAL NUMBER OF ATOMS.
Crystal growpH: 4.8
Details: 37% (V/V) ETHANOL, 450 MM NACL, 50 MM CITRATE BUFFER PH4.8, 1MM EDTA, USING THE DIALYSIS METHOD., pH 4.80
Crystal grow
*PLUS
Method: other / Details: Glykos, N.M., (1999) Acta Cryst., D55, 1301.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1999 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→36 Å / Num. obs: 8771 / % possible obs: 96.4 % / Redundancy: 8.2 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.1 / % possible all: 91.6
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 36 Å
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
Queen of Spadesphasing
X-PLORphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLY-ALANINE MODEL OF ONE HELIX (RESIDUES 4-29) FROM PDB ENTRY 1RPO

1rpo


Resolution: 1.9→36 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESOLUTION-DEPENDENT TWO-LINE WEIGHTING SCHEME (DAVID SMITH, G. (1997), ACTA CRYST. D53, PP.41-48).
RfactorNum. reflection% reflectionSelection details
Rfree0.232 489 5 %RANDOM
Rwork0.187 ---
obs0.187 8771 96.4 %-
Displacement parametersBiso mean: 41.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.7123 Å20 Å20 Å2
2--1.7505 Å20 Å2
3----4.4628 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 36 Å
Refinement stepCycle: LAST / Resolution: 1.9→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 0 92 943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.864
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.031
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it7.957
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.323 69 5 %
Rwork0.192 953 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1TOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
X-RAY DIFFRACTION3PROTEIN_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 36 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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