HEADER PEPTIDE BINDING PROTEIN 18-SEP-20 7D34 TITLE ATCLPS1-PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS1, COMPND 3 CHLOROPLASTIC; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: CPLS1, CLPT, AT1G68660, F24J5.10, F24J5.4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARABIDOPSIS THALIANA, CLPS, N-DEGRON PATHWAY, COMPLEX STRUCTURE, KEYWDS 2 PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HEO,L.KIM,D.H.KWON,H.K.SONG REVDAT 2 29-NOV-23 7D34 1 REMARK REVDAT 1 28-APR-21 7D34 0 JRNL AUTH L.KIM,J.HEO,D.H.KWON,J.S.SHIN,S.H.JANG,Z.Y.PARK,H.K.SONG JRNL TITL STRUCTURAL BASIS FOR THE N-DEGRON SPECIFICITY OF CLPS1 FROM JRNL TITL 2 ARABIDOPSIS THALIANA. JRNL REF PROTEIN SCI. V. 30 700 2021 JRNL REFN ESSN 1469-896X JRNL PMID 33368743 JRNL DOI 10.1002/PRO.4018 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 12954 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.274 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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 34.4100 - 4.1728 1.00 1431 159 0.2281 0.2281 REMARK 3 2 4.1728 - 3.3129 0.98 1323 148 0.2428 0.2903 REMARK 3 3 3.3129 - 2.8944 1.00 1321 147 0.2949 0.3172 REMARK 3 4 2.8944 - 2.6298 0.99 1318 147 0.3100 0.3420 REMARK 3 5 2.6298 - 2.4414 0.99 1302 143 0.3096 0.3422 REMARK 3 6 2.4414 - 2.2975 0.99 1292 142 0.3102 0.3446 REMARK 3 7 2.2975 - 2.1825 0.94 1209 135 0.3298 0.3742 REMARK 3 8 2.1825 - 2.0875 0.97 1270 137 0.3373 0.3587 REMARK 3 9 2.0875 - 2.0071 0.93 1196 134 0.3169 0.3717 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.009 1245 REMARK 3 ANGLE : 1.025 1689 REMARK 3 CHIRALITY : 0.054 198 REMARK 3 PLANARITY : 0.006 225 REMARK 3 DIHEDRAL : 15.377 759 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 13.5346 4.0995 14.6048 REMARK 3 T TENSOR REMARK 3 T11: 0.2672 T22: 0.2581 REMARK 3 T33: 0.2271 T12: -0.0143 REMARK 3 T13: -0.0868 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 3.9617 L22: 0.5582 REMARK 3 L33: 1.2202 L12: 0.8158 REMARK 3 L13: -0.2327 L23: 0.0385 REMARK 3 S TENSOR REMARK 3 S11: 0.0944 S12: -0.6675 S13: -0.1064 REMARK 3 S21: 0.1448 S22: -0.0807 S23: -0.0629 REMARK 3 S31: 0.0144 S32: -0.0860 S33: -0.0099 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 7D34 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13209 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 4O2X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6 REMARK 280 (HAMPTON RESEARCH, HR2-731), 2 M NACL (HAMPTON RESEARCH, HR2-637) REMARK 280 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 40.52800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.00250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.52800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.00250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 157 REMARK 465 GLY A 158 REMARK 465 CYS A 159 REMARK 465 GLY B 157 REMARK 465 GLY B 158 REMARK 465 CYS B 159 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH11 ARG B 83 OE2 GLU B 153 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 PHE B 91 -54.20 -121.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ALA A 203 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PHE A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ALA A 203 DBREF 7D34 A 79 159 UNP Q9SX29 CLPS1_ARATH 79 159 DBREF 7D34 B 79 159 UNP Q9SX29 CLPS1_ARATH 79 159 SEQADV 7D34 LEU A 78 UNP Q9SX29 EXPRESSION TAG SEQADV 7D34 LEU B 78 UNP Q9SX29 EXPRESSION TAG SEQRES 1 A 82 LEU ALA PRO PRO TYR ARG VAL ILE LEU HIS ASN ASP ASN SEQRES 2 A 82 PHE ASN LYS ARG GLU TYR VAL VAL GLN VAL LEU MET LYS SEQRES 3 A 82 VAL ILE PRO GLY MET THR VAL ASP ASN ALA VAL ASN ILE SEQRES 4 A 82 MET GLN GLU ALA HIS ILE ASN GLY LEU ALA VAL VAL ILE SEQRES 5 A 82 VAL CYS ALA GLN ALA ASP ALA GLU GLN HIS CYS MET GLN SEQRES 6 A 82 LEU ARG GLY ASN GLY LEU LEU SER SER VAL GLU PRO ASP SEQRES 7 A 82 GLY GLY GLY CYS SEQRES 1 B 82 LEU ALA PRO PRO TYR ARG VAL ILE LEU HIS ASN ASP ASN SEQRES 2 B 82 PHE ASN LYS ARG GLU TYR VAL VAL GLN VAL LEU MET LYS SEQRES 3 B 82 VAL ILE PRO GLY MET THR VAL ASP ASN ALA VAL ASN ILE SEQRES 4 B 82 MET GLN GLU ALA HIS ILE ASN GLY LEU ALA VAL VAL ILE SEQRES 5 B 82 VAL CYS ALA GLN ALA ASP ALA GLU GLN HIS CYS MET GLN SEQRES 6 B 82 LEU ARG GLY ASN GLY LEU LEU SER SER VAL GLU PRO ASP SEQRES 7 B 82 GLY GLY GLY CYS HET ACY A 201 7 HET PHE A 202 22 HET ALA A 203 7 HETNAM ACY ACETIC ACID HETNAM PHE PHENYLALANINE HETNAM ALA ALANINE FORMUL 3 ACY C2 H4 O2 FORMUL 4 PHE C9 H11 N O2 FORMUL 5 ALA C3 H7 N O2 FORMUL 6 HOH *12(H2 O) HELIX 1 AA1 LYS A 93 ILE A 105 1 13 HELIX 2 AA2 THR A 109 GLY A 124 1 16 HELIX 3 AA3 ALA A 132 ASN A 146 1 15 HELIX 4 AA4 LYS B 93 ILE B 105 1 13 HELIX 5 AA5 THR B 109 GLY B 124 1 16 HELIX 6 AA6 GLN B 133 ASN B 146 1 14 SHEET 1 AA1 3 LEU A 125 CYS A 131 0 SHEET 2 AA1 3 TYR A 82 HIS A 87 -1 N VAL A 84 O VAL A 128 SHEET 3 AA1 3 LEU A 149 PRO A 154 -1 O GLU A 153 N ARG A 83 SHEET 1 AA2 3 LEU B 125 ALA B 132 0 SHEET 2 AA2 3 PRO B 81 HIS B 87 -1 N VAL B 84 O VAL B 128 SHEET 3 AA2 3 SER B 150 PRO B 154 -1 O SER B 151 N ILE B 85 LINK C PHE A 202 N ALA A 203 1555 1555 1.34 SITE 1 AC1 3 ASN A 92 ALA A 134 GLY A 147 SITE 1 AC2 7 ASN A 88 ASP A 89 ASN A 92 VAL A 97 SITE 2 AC2 7 MET A 117 HIS A 121 ALA A 203 SITE 1 AC3 4 ASN A 92 LYS A 93 ARG A 94 PHE A 202 CRYST1 81.056 38.005 61.411 90.00 90.00 90.00 P 21 21 2 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 0.012337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016284 0.00000