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Open data
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Basic information
Entry | Database: PDB / ID: 1gmg | ||||||
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Title | ALANINE 31 PROLINE MUTANT OF ROP PROTEIN, MONOCLINIC FORM | ||||||
![]() | REGULATORY PROTEIN ROP | ||||||
![]() | TRANSCRIPTION REGULATION | ||||||
Function / homology | Helix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Glykos, N.M. / Kokkinidis, M. | ||||||
![]() | ![]() Title: Structure Determination of a Small Protein Through a 23-Dimensional Molecular-Replacement Search. Authors: Glykos, N.M. / Kokkinidis, M. #1: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.1 KB | Display | ![]() |
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PDB format | ![]() | 24.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.5 KB | Display | ![]() |
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Full document | ![]() | 416.1 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 9.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rpoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99579, 0.02097, 0.0892), Vector: Details | THE 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 | Mass: 7263.076 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density 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. |
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Crystal grow | pH: 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. |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1999 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: POLY-ALANINE MODEL OF ONE HELIX (RESIDUES 4-29) FROM PDB ENTRY 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).
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Displacement parameters | Biso mean: 41.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |