PDB Short entry for 3KZ3 HEADER TRANSCRIPTION 07-DEC-09 3KZ3 TITLE A STRUCTURE OF A LAMBDA REPRESSOR FRAGMENT MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPRESSOR PROTEIN CI; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 8-85; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE LAMBDA; SOURCE 4 ORGANISM_TAXID: 10710; SOURCE 5 GENE: CI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: ROSETTA KEYWDS FIVE HELIX BUNDLE, DNA-BINDING, REPRESSOR, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.GRUEBELE,F.LIU,Y.GAO REVDAT 4 21-FEB-24 3KZ3 1 REMARK REVDAT 3 13-OCT-21 3KZ3 1 SEQADV REVDAT 2 07-APR-10 3KZ3 1 JRNL REVDAT 1 23-FEB-10 3KZ3 0 JRNL AUTH F.LIU,Y.G.GAO,M.GRUEBELE JRNL TITL A SURVEY OF LAMBDA REPRESSOR FRAGMENTS FROM TWO-STATE TO JRNL TITL 2 DOWNHILL FOLDING. JRNL REF J.MOL.BIOL. V. 397 789 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20138892 JRNL DOI 10.1016/J.JMB.2010.01.071 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.193 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.189 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18248 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.189 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.188 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 17329 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1236 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 282 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 1.957 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.022 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.036 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.043 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.070 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE REMARK 4 REMARK 4 3KZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000056627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19544 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.35500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 15 CD - NE - CZ ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 VAL B 35 CA - CB - CG2 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG B 81 CD - NE - CZ ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG B 81 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LMB RELATED DB: PDB REMARK 900 STRUCTURE OF WILD TYPE LAMBDA REPRESSOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHORS, THE PROTEIN WAS DERIVED FROM OAS TG'S REMARK 999 LAMBDA REPRESSOR PROTEIN EXPRESSION VECTOR WHICH CARRIES THE CHANGE REMARK 999 OF THE FIRST N-TERM AND THE LAST C-TERM RESIDUES. THESE TWO CHANGES REMARK 999 CAME FROM THE PREPARATION OF THE EXPRESSION SYSTEM, POSSIBLY THE REMARK 999 RESTRICTION ENZYME DIGESTION SITE DESIGN WHEN THE DNA SEQUENCE WAS REMARK 999 CUT FROM THE WILD-TYPE PROTEIN AND INSERTED INTO THE VECTOR DBREF 3KZ3 A 6 83 UNP P03034 RPC1_LAMBD 8 85 DBREF 3KZ3 B 6 83 UNP P03034 RPC1_LAMBD 8 85 SEQADV 3KZ3 SER A 5 UNP P03034 SEE REMARK 999 SEQADV 3KZ3 TRP A 21 UNP P03034 TYR 23 ENGINEERED MUTATION SEQADV 3KZ3 TYR A 32 UNP P03034 GLN 34 ENGINEERED MUTATION SEQADV 3KZ3 ALA A 45 UNP P03034 GLY 47 ENGINEERED MUTATION SEQADV 3KZ3 ALA A 47 UNP P03034 GLY 49 ENGINEERED MUTATION SEQADV 3KZ3 ARG A 84 UNP P03034 SEE REMARK 999 SEQADV 3KZ3 SER B 5 UNP P03034 SEE REMARK 999 SEQADV 3KZ3 TRP B 21 UNP P03034 TYR 23 ENGINEERED MUTATION SEQADV 3KZ3 TYR B 32 UNP P03034 GLN 34 ENGINEERED MUTATION SEQADV 3KZ3 ALA B 45 UNP P03034 GLY 47 ENGINEERED MUTATION SEQADV 3KZ3 ALA B 47 UNP P03034 GLY 49 ENGINEERED MUTATION SEQADV 3KZ3 ARG B 84 UNP P03034 SEE REMARK 999 SEQRES 1 A 80 SER LEU THR GLN GLU GLN LEU GLU ASP ALA ARG ARG LEU SEQRES 2 A 80 LYS ALA ILE TRP GLU LYS LYS LYS ASN GLU LEU GLY LEU SEQRES 3 A 80 SER TYR GLU SER VAL ALA ASP LYS MET GLY MET GLY GLN SEQRES 4 A 80 SER ALA VAL ALA ALA LEU PHE ASN GLY ILE ASN ALA LEU SEQRES 5 A 80 ASN ALA TYR ASN ALA ALA LEU LEU ALA LYS ILE LEU LYS SEQRES 6 A 80 VAL SER VAL GLU GLU PHE SER PRO SER ILE ALA ARG GLU SEQRES 7 A 80 ILE ARG SEQRES 1 B 80 SER LEU THR GLN GLU GLN LEU GLU ASP ALA ARG ARG LEU SEQRES 2 B 80 LYS ALA ILE TRP GLU LYS LYS LYS ASN GLU LEU GLY LEU SEQRES 3 B 80 SER TYR GLU SER VAL ALA ASP LYS MET GLY MET GLY GLN SEQRES 4 B 80 SER ALA VAL ALA ALA LEU PHE ASN GLY ILE ASN ALA LEU SEQRES 5 B 80 ASN ALA TYR ASN ALA ALA LEU LEU ALA LYS ILE LEU LYS SEQRES 6 B 80 VAL SER VAL GLU GLU PHE SER PRO SER ILE ALA ARG GLU SEQRES 7 B 80 ILE ARG FORMUL 3 HOH *282(H2 O) HELIX 1 1 THR A 7 GLY A 29 1 23 HELIX 2 2 SER A 31 MET A 39 1 9 HELIX 3 3 GLY A 42 ASN A 51 1 10 HELIX 4 4 ASN A 57 LYS A 69 1 13 HELIX 5 5 SER A 71 PHE A 75 5 5 HELIX 6 6 SER A 76 ARG A 84 1 9 HELIX 7 7 THR B 7 GLY B 29 1 23 HELIX 8 8 SER B 31 GLY B 40 1 10 HELIX 9 9 GLY B 42 ASN B 51 1 10 HELIX 10 10 ASN B 57 LYS B 69 1 13 HELIX 11 11 SER B 71 PHE B 75 5 5 HELIX 12 12 SER B 76 ARG B 84 1 9 CRYST1 32.630 58.710 42.850 90.00 98.18 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.030647 0.000000 0.004405 0.00000 SCALE2 0.000000 0.017033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023577 0.00000