HEADER PEPTIDE BINDING PROTEIN 02-JUL-08 3DNJ TITLE THE STRUCTURE OF THE CAULOBACTER CRESCENTUS CLPS PROTEASE ADAPTOR TITLE 2 PROTEIN IN COMPLEX WITH A N-END RULE PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SYNTHETIC N-END RULE PEPTIDE; COMPND 7 CHAIN: C, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER VIBRIOIDES; SOURCE 3 ORGANISM_COMMON: CAULOBACTER VIBRIOIDES; SOURCE 4 ORGANISM_TAXID: 155892; SOURCE 5 STRAIN: CB15; SOURCE 6 GENE: CLPS, CC_2467; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET23B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THE PEPTIDE IS CHEMICALLY SYNTHESIZED KEYWDS ADAPTOR, PROTEIN-PEPTIDE COMPLEX, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.WANG,G.ROMAN-HERNANDEZ,R.A.GRANT,R.T.SAUER,T.A.BAKER REVDAT 5 03-APR-24 3DNJ 1 REMARK REVDAT 4 21-FEB-24 3DNJ 1 REMARK LINK REVDAT 3 25-OCT-17 3DNJ 1 REMARK REVDAT 2 24-FEB-09 3DNJ 1 VERSN REVDAT 1 18-NOV-08 3DNJ 0 JRNL AUTH K.H.WANG,G.ROMAN-HERNANDEZ,R.A.GRANT,R.T.SAUER,T.A.BAKER JRNL TITL THE MOLECULAR BASIS OF N-END RULE RECOGNITION. JRNL REF MOL.CELL V. 32 406 2008 JRNL REFN ISSN 1097-2765 JRNL PMID 18995838 JRNL DOI 10.1016/J.MOLCEL.2008.08.032 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 51076 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2538 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 14.8770 - 3.0060 0.92 2668 131 0.1760 0.1850 REMARK 3 2 3.0060 - 2.3890 1.00 2817 172 0.1510 0.1740 REMARK 3 3 2.3890 - 2.0880 1.00 2845 132 0.1350 0.1520 REMARK 3 4 2.0880 - 1.8980 1.00 2841 142 0.1270 0.1580 REMARK 3 5 1.8980 - 1.7620 1.00 2829 132 0.1320 0.1610 REMARK 3 6 1.7620 - 1.6580 1.00 2812 163 0.1220 0.1480 REMARK 3 7 1.6580 - 1.5750 1.00 2815 162 0.1090 0.1400 REMARK 3 8 1.5750 - 1.5070 1.00 2812 147 0.1000 0.1190 REMARK 3 9 1.5070 - 1.4490 1.00 2804 136 0.0980 0.1270 REMARK 3 10 1.4490 - 1.3990 1.00 2825 145 0.0960 0.1380 REMARK 3 11 1.3990 - 1.3550 1.00 2822 138 0.0960 0.1250 REMARK 3 12 1.3550 - 1.3160 1.00 2806 149 0.0940 0.1340 REMARK 3 13 1.3160 - 1.2820 1.00 2797 156 0.0950 0.1340 REMARK 3 14 1.2820 - 1.2500 1.00 2781 162 0.1000 0.1310 REMARK 3 15 1.2500 - 1.2220 0.98 2780 150 0.1070 0.1570 REMARK 3 16 1.2220 - 1.1960 0.90 2531 117 0.1140 0.1410 REMARK 3 17 1.1960 - 1.1720 0.76 2131 109 0.1140 0.1580 REMARK 3 18 1.1720 - 1.1500 0.65 1822 95 0.1160 0.1380 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : 0.45 REMARK 3 B_SOL : 58.16 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84300 REMARK 3 B22 (A**2) : -1.73900 REMARK 3 B33 (A**2) : -2.14800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.03900 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 : 0.006 3063 REMARK 3 ANGLE : 0.876 5548 REMARK 3 CHIRALITY : 0.062 236 REMARK 3 PLANARITY : 0.005 470 REMARK 3 DIHEDRAL : 14.713 796 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 3DNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97927 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51120 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.19400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1R60 CHAIN C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5 0.2 M MGCL2 13% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 26.98700 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 THR A 35 REMARK 465 GLN A 36 REMARK 465 LYS A 37 REMARK 465 PRO A 38 REMARK 465 SER A 39 REMARK 465 THR B 35 REMARK 465 GLN B 36 REMARK 465 LYS B 37 REMARK 465 PRO B 38 REMARK 465 VAL C 4 REMARK 465 GLN C 5 REMARK 465 ARG C 6 REMARK 465 ASP C 7 REMARK 465 SER C 8 REMARK 465 LYS C 9 REMARK 465 GLU C 10 REMARK 465 VAL D 4 REMARK 465 GLN D 5 REMARK 465 ARG D 6 REMARK 465 ASP D 7 REMARK 465 SER D 8 REMARK 465 LYS D 9 REMARK 465 GLU D 10 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 PHE C 3 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE D 3 CG CD1 CD2 CE1 CE2 CZ 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 TYR B 50 -37.64 -142.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 O REMARK 620 2 HOH A 209 O 89.6 REMARK 620 3 ASP B 119 O 87.0 172.7 REMARK 620 4 HOH B 207 O 95.0 106.3 80.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1 DBREF 3DNJ A 35 119 UNP Q9A5I0 CLPS_CAUCR 35 119 DBREF 3DNJ B 35 119 UNP Q9A5I0 CLPS_CAUCR 35 119 DBREF 3DNJ C 1 10 PDB 3DNJ 3DNJ 1 10 DBREF 3DNJ D 1 10 PDB 3DNJ 3DNJ 1 10 SEQRES 1 A 85 THR GLN LYS PRO SER LEU TYR ARG VAL LEU ILE LEU ASN SEQRES 2 A 85 ASP ASP TYR THR PRO MET GLU PHE VAL VAL TYR VAL LEU SEQRES 3 A 85 GLU ARG PHE PHE ASN LYS SER ARG GLU ASP ALA THR ARG SEQRES 4 A 85 ILE MET LEU HIS VAL HIS GLN ASN GLY VAL GLY VAL CYS SEQRES 5 A 85 GLY VAL TYR THR TYR GLU VAL ALA GLU THR LYS VAL ALA SEQRES 6 A 85 GLN VAL ILE ASP SER ALA ARG ARG HIS GLN HIS PRO LEU SEQRES 7 A 85 GLN CYS THR MET GLU LYS ASP SEQRES 1 B 85 THR GLN LYS PRO SER LEU TYR ARG VAL LEU ILE LEU ASN SEQRES 2 B 85 ASP ASP TYR THR PRO MET GLU PHE VAL VAL TYR VAL LEU SEQRES 3 B 85 GLU ARG PHE PHE ASN LYS SER ARG GLU ASP ALA THR ARG SEQRES 4 B 85 ILE MET LEU HIS VAL HIS GLN ASN GLY VAL GLY VAL CYS SEQRES 5 B 85 GLY VAL TYR THR TYR GLU VAL ALA GLU THR LYS VAL ALA SEQRES 6 B 85 GLN VAL ILE ASP SER ALA ARG ARG HIS GLN HIS PRO LEU SEQRES 7 B 85 GLN CYS THR MET GLU LYS ASP SEQRES 1 C 10 TYR LEU PHE VAL GLN ARG ASP SER LYS GLU SEQRES 1 D 10 TYR LEU PHE VAL GLN ARG ASP SER LYS GLU HET MG A 1 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG MG 2+ FORMUL 6 HOH *283(H2 O) HELIX 1 1 PRO A 52 ASN A 65 1 14 HELIX 2 2 SER A 67 GLY A 82 1 16 HELIX 3 3 THR A 90 HIS A 108 1 19 HELIX 4 4 PRO B 52 PHE B 64 1 13 HELIX 5 5 SER B 67 GLY B 82 1 16 HELIX 6 6 TYR B 91 HIS B 108 1 18 SHEET 1 A 3 VAL A 83 TYR A 89 0 SHEET 2 A 3 TYR A 41 LEU A 46 -1 N VAL A 43 O CYS A 86 SHEET 3 A 3 CYS A 114 LYS A 118 -1 O THR A 115 N LEU A 44 SHEET 1 B 3 VAL B 83 THR B 90 0 SHEET 2 B 3 LEU B 40 LEU B 46 -1 N VAL B 43 O CYS B 86 SHEET 3 B 3 CYS B 114 LYS B 118 -1 O THR B 115 N LEU B 44 LINK MG MG A 1 O ASP A 119 1555 1555 2.15 LINK MG MG A 1 O HOH A 209 1555 1555 2.49 LINK MG MG A 1 O ASP B 119 1555 1555 2.12 LINK MG MG A 1 O HOH B 207 1555 1555 2.45 SITE 1 AC1 2 ASP A 119 ASP B 119 CRYST1 33.693 53.974 44.824 90.00 110.39 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 0.029680 0.000000 0.011032 0.00000 SCALE2 0.000000 0.018527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023801 0.00000