HEADER RIBOSOMAL PROTEIN 24-MAY-10 3N4Z TITLE CRYSTAL STRUCTURE OF QUINTUPLE ARG-TO-LYS VARIANT OF T. CELER L30E COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L30E; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS CELER; SOURCE 3 ORGANISM_TAXID: 2264; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: C41; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3C KEYWDS RIBOSOMAL PROTEIN, L30E, QUINTUPLE, ARG-TO-LYS EXPDTA X-RAY DIFFRACTION AUTHOR C.H.CHAN,K.B.WONG REVDAT 4 01-NOV-23 3N4Z 1 SEQADV REVDAT 3 27-JUN-12 3N4Z 1 JRNL REVDAT 2 01-FEB-12 3N4Z 1 JRNL VERSN REVDAT 1 09-JUN-10 3N4Z 0 JRNL AUTH C.H.CHAN,C.C.WILBANKS,G.I.MAKHATADZE,K.B.WONG JRNL TITL ELECTROSTATIC CONTRIBUTION OF SURFACE CHARGE RESIDUES TO THE JRNL TITL 2 STABILITY OF A THERMOPHILIC PROTEIN: BENCHMARKING JRNL TITL 3 EXPERIMENTAL AND PREDICTED PKA VALUES JRNL REF PLOS ONE V. 7 30296 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22279578 JRNL DOI 10.1371/JOURNAL.PONE.0030296 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.880 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8032 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 803 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.4897 - 4.3427 1.00 1282 143 0.1807 0.2262 REMARK 3 2 4.3427 - 3.4532 1.00 1221 134 0.1495 0.2038 REMARK 3 3 3.4532 - 3.0185 1.00 1196 134 0.1614 0.2679 REMARK 3 4 3.0185 - 2.7433 1.00 1174 130 0.1730 0.2754 REMARK 3 5 2.7433 - 2.5472 1.00 1168 130 0.1808 0.2645 REMARK 3 6 2.5472 - 2.3973 0.99 1188 132 0.1874 0.2548 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 82.83 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.800 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.28380 REMARK 3 B22 (A**2) : -3.08270 REMARK 3 B33 (A**2) : 7.36650 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1449 REMARK 3 ANGLE : 1.069 1960 REMARK 3 CHIRALITY : 0.067 233 REMARK 3 PLANARITY : 0.003 248 REMARK 3 DIHEDRAL : 14.562 518 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3N4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000059386. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-09; 22-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 110; 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; N REMARK 200 RADIATION SOURCE : ROTATING ANODE; ROTATING ANODE REMARK 200 BEAMLINE : NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007; RIGAKU REMARK 200 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.5418 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV; RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.397 REMARK 200 RESOLUTION RANGE LOW (A) : 39.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.70 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1H7M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M POTASSIUM PHOSPHATE, 0.8M SODIUM REMARK 280 PHOSPHATE, 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.38350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.68000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.38350 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 98 REMARK 465 LYS A 99 REMARK 465 GLU A 100 REMARK 465 MET B 0 REMARK 465 GLY B 98 REMARK 465 LYS B 99 REMARK 465 GLU B 100 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 LYS A 15 CG CD CE NZ REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 ILE A 45 CG1 CG2 CD1 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 GLY A 97 CA C O REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 ARG B 39 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 54 CG CD CE NZ REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 GLU B 90 CG CD OE1 OE2 REMARK 470 GLY B 97 CA C O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU B 96 154.88 -38.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H7M RELATED DB: PDB REMARK 900 WILD-TYPE PROTEIN REMARK 900 RELATED ID: 3N4Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WILD-TYPE T. CELER L30E IN LOW IONIC STRENGTH REMARK 900 CONDITION WITHOUT PRECIPITANT DBREF 3N4Z A 0 100 UNP P29160 RL30E_THECE 1 101 DBREF 3N4Z B 0 100 UNP P29160 RL30E_THECE 1 101 SEQADV 3N4Z LYS A 8 UNP P29160 ARG 9 ENGINEERED MUTATION SEQADV 3N4Z LYS A 21 UNP P29160 ARG 22 ENGINEERED MUTATION SEQADV 3N4Z LYS A 42 UNP P29160 ARG 43 ENGINEERED MUTATION SEQADV 3N4Z LYS A 54 UNP P29160 ARG 55 ENGINEERED MUTATION SEQADV 3N4Z LYS A 76 UNP P29160 ARG 77 ENGINEERED MUTATION SEQADV 3N4Z LYS B 8 UNP P29160 ARG 9 ENGINEERED MUTATION SEQADV 3N4Z LYS B 21 UNP P29160 ARG 22 ENGINEERED MUTATION SEQADV 3N4Z LYS B 42 UNP P29160 ARG 43 ENGINEERED MUTATION SEQADV 3N4Z LYS B 54 UNP P29160 ARG 55 ENGINEERED MUTATION SEQADV 3N4Z LYS B 76 UNP P29160 ARG 77 ENGINEERED MUTATION SEQRES 1 A 101 MET VAL ASP PHE ALA PHE GLU LEU LYS LYS ALA GLN ASP SEQRES 2 A 101 THR GLY LYS ILE VAL MET GLY ALA LYS LYS SER ILE GLN SEQRES 3 A 101 TYR ALA LYS MET GLY GLY ALA LYS LEU ILE ILE VAL ALA SEQRES 4 A 101 ARG ASN ALA LYS PRO ASP ILE LYS GLU ASP ILE GLU TYR SEQRES 5 A 101 TYR ALA LYS LEU SER GLY ILE PRO VAL TYR GLU PHE GLU SEQRES 6 A 101 GLY THR SER VAL GLU LEU GLY THR LEU LEU GLY LYS PRO SEQRES 7 A 101 HIS THR VAL SER ALA LEU ALA VAL VAL ASP PRO GLY GLU SEQRES 8 A 101 SER ARG ILE LEU ALA LEU GLY GLY LYS GLU SEQRES 1 B 101 MET VAL ASP PHE ALA PHE GLU LEU LYS LYS ALA GLN ASP SEQRES 2 B 101 THR GLY LYS ILE VAL MET GLY ALA LYS LYS SER ILE GLN SEQRES 3 B 101 TYR ALA LYS MET GLY GLY ALA LYS LEU ILE ILE VAL ALA SEQRES 4 B 101 ARG ASN ALA LYS PRO ASP ILE LYS GLU ASP ILE GLU TYR SEQRES 5 B 101 TYR ALA LYS LEU SER GLY ILE PRO VAL TYR GLU PHE GLU SEQRES 6 B 101 GLY THR SER VAL GLU LEU GLY THR LEU LEU GLY LYS PRO SEQRES 7 B 101 HIS THR VAL SER ALA LEU ALA VAL VAL ASP PRO GLY GLU SEQRES 8 B 101 SER ARG ILE LEU ALA LEU GLY GLY LYS GLU FORMUL 3 HOH *114(H2 O) HELIX 1 1 ASP A 2 GLY A 14 1 13 HELIX 2 2 GLY A 19 GLY A 30 1 12 HELIX 3 3 LYS A 42 GLY A 57 1 16 HELIX 4 4 THR A 66 LEU A 74 1 9 HELIX 5 5 ARG A 92 LEU A 96 5 5 HELIX 6 6 ASP B 2 GLY B 14 1 13 HELIX 7 7 GLY B 19 GLY B 30 1 12 HELIX 8 8 LYS B 42 GLY B 57 1 16 HELIX 9 9 THR B 66 LEU B 74 1 9 HELIX 10 10 ARG B 92 LEU B 96 5 5 SHEET 1 A 4 LYS A 15 MET A 18 0 SHEET 2 A 4 ALA A 82 ASP A 87 -1 O ALA A 84 N VAL A 17 SHEET 3 A 4 LEU A 34 ALA A 38 -1 N LEU A 34 O VAL A 85 SHEET 4 A 4 VAL A 60 PHE A 63 1 O TYR A 61 N ILE A 35 SHEET 1 B 4 LYS B 15 MET B 18 0 SHEET 2 B 4 ALA B 82 ASP B 87 -1 O ALA B 84 N VAL B 17 SHEET 3 B 4 LEU B 34 ALA B 38 -1 N LEU B 34 O VAL B 85 SHEET 4 B 4 VAL B 60 PHE B 63 1 O TYR B 61 N ILE B 35 CRYST1 30.487 61.360 102.767 90.00 90.00 90.00 P 2 21 21 8 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 0.032800 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009731 0.00000