HEADER MOTOR PROTEIN 29-AUG-23 8U0X TITLE YEAST PEX6 N1(1-184) DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOMAL ATPASE PEX6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEROXIN-6,PEROXISOMAL ASSEMBLY PROTEIN 8; COMPND 5 EC: 3.6.4.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: PEX6, PAS8, YNL329C, N0310; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-TERMINAL DOMAIN AAA-ATPASE PEX6, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.M.GARDNER,B.A.ALI REVDAT 3 10-JAN-24 8U0X 1 JRNL REVDAT 2 13-DEC-23 8U0X 1 JRNL REVDAT 1 29-NOV-23 8U0X 0 JRNL AUTH B.A.ALI,R.M.JUDY,S.CHOWDHURY,N.K.JACOBSEN,D.T.CASTANZO, JRNL AUTH 2 K.L.CARR,C.D.RICHARDSON,G.C.LANDER,A.MARTIN,B.M.GARDNER JRNL TITL THE N1 DOMAIN OF THE PEROXISOMAL AAA-ATPASE PEX6 IS REQUIRED JRNL TITL 2 FOR PEX15 BINDING AND PROPER ASSEMBLY WITH PEX1. JRNL REF J.BIOL.CHEM. V. 300 05504 2023 JRNL REFN ESSN 1083-351X JRNL PMID 38036174 JRNL DOI 10.1016/J.JBC.2023.105504 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18306 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 951 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 73.8900 - 3.5700 1.00 2597 135 0.1932 0.2380 REMARK 3 2 3.5600 - 2.8300 1.00 2475 155 0.2049 0.2491 REMARK 3 3 2.8300 - 2.4700 1.00 2470 130 0.2242 0.2492 REMARK 3 4 2.4700 - 2.2500 1.00 2454 134 0.2379 0.2906 REMARK 3 5 2.2400 - 2.0800 1.00 2459 122 0.2249 0.2539 REMARK 3 6 2.0800 - 1.9600 1.00 2444 140 0.2265 0.3004 REMARK 3 7 1.9600 - 1.8600 1.00 2456 135 0.2781 0.3458 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.251 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.489 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.38 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 : 0.008 1423 REMARK 3 ANGLE : 0.999 1937 REMARK 3 CHIRALITY : 0.062 223 REMARK 3 PLANARITY : 0.007 247 REMARK 3 DIHEDRAL : 5.988 187 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 8U0X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000274361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1158 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 73.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.36100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M LICL, 0.1 M CITRIC ACID PH 5, REMARK 280 16% PEG6000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: MONOMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 206 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 THR A 176 REMARK 465 GLU A 177 REMARK 465 GLN A 178 REMARK 465 LYS A 179 REMARK 465 LEU A 180 REMARK 465 SER A 181 REMARK 465 ALA A 182 REMARK 465 LEU A 183 REMARK 465 LYS A 184 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 O HOH A 254 O HOH A 262 1.70 REMARK 500 O HOH A 271 O HOH A 285 2.05 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 TYR A 43 104.34 -59.01 REMARK 500 THR A 81 -91.29 -145.40 REMARK 500 GLU A 136 -59.60 -153.77 REMARK 500 ARG A 142 -1.35 76.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 8U0X A 1 184 UNP P33760 PEX6_YEAST 1 184 SEQADV 8U0X GLY A -1 UNP P33760 EXPRESSION TAG SEQADV 8U0X PRO A 0 UNP P33760 EXPRESSION TAG SEQRES 1 A 186 GLY PRO MET LYS ALA SER LEU THR PHE SER LEU SER GLY SEQRES 2 A 186 ILE TYR ALA PRO CYS SER ILE SER ARG ASP ILE TYR LEU SEQRES 3 A 186 GLU TYR GLY ASP LYS LYS ALA GLU CYS LEU TYR GLY THR SEQRES 4 A 186 ILE ARG LEU PRO GLN TYR GLY PRO GLY CYS THR PRO GLY SEQRES 5 A 186 LYS ILE VAL HIS CYS VAL LEU ASP ASP SER LEU PRO PHE SEQRES 6 A 186 CYS SER ILE VAL VAL PRO SER LYS LEU PHE GLY PHE MET SEQRES 7 A 186 PRO THR GLN PRO THR MET ASP PHE CYS TYR PHE GLU PRO SEQRES 8 A 186 ILE LEU ASP ASN VAL VAL PRO VAL LEU ASP SER VAL THR SEQRES 9 A 186 PHE LEU ILE ASN GLU GLN LEU TYR SER LYS LEU MET ASP SEQRES 10 A 186 LEU PRO GLN GLU MET GLN GLN ILE GLN PHE LEU HIS TYR SEQRES 11 A 186 LYS TYR ASN ILE ASN SER MET GLU THR VAL VAL HIS SER SEQRES 12 A 186 ARG ASP ILE LEU THR SER GLY LEU CYS GLN ILE LEU ASN SEQRES 13 A 186 CYS SER PRO PHE PRO GLN GLY LEU VAL ASP PHE THR GLU SEQRES 14 A 186 THR GLN LEU ILE LEU VAL ASN ASP THR GLU GLN LYS LEU SEQRES 15 A 186 SER ALA LEU LYS FORMUL 2 HOH *91(H2 O) HELIX 1 AA1 SER A 19 GLU A 25 1 7 HELIX 2 AA2 LYS A 71 PHE A 73 5 3 HELIX 3 AA3 ASN A 106 ASP A 115 1 10 HELIX 4 AA4 GLN A 118 ASN A 131 1 14 SHEET 1 AA1 7 MET A 1 SER A 8 0 SHEET 2 AA1 7 SER A 65 PRO A 69 1 O VAL A 68 N THR A 6 SHEET 3 AA1 7 CYS A 16 ILE A 18 -1 N SER A 17 O VAL A 67 SHEET 4 AA1 7 LYS A 51 LEU A 57 1 O VAL A 56 N CYS A 16 SHEET 5 AA1 7 LEU A 34 ARG A 39 -1 N GLY A 36 O VAL A 53 SHEET 6 AA1 7 PHE A 84 PRO A 89 -1 O TYR A 86 N ARG A 39 SHEET 7 AA1 7 MET A 1 SER A 8 -1 N MET A 1 O PHE A 87 SHEET 1 AA2 4 ILE A 144 THR A 146 0 SHEET 2 AA2 4 CYS A 150 SER A 156 -1 N CYS A 150 O THR A 146 SHEET 3 AA2 4 SER A 100 ILE A 105 -1 N THR A 102 O LEU A 153 SHEET 4 AA2 4 GLN A 169 ASN A 174 1 O ILE A 171 N PHE A 103 SHEET 1 AA3 2 VAL A 138 HIS A 140 0 SHEET 2 AA3 2 GLN A 160 LEU A 162 -1 O GLY A 161 N VAL A 139 CISPEP 1 SER A 156 PRO A 157 0 2.15 CRYST1 85.317 85.317 51.192 90.00 90.00 120.00 P 3 2 1 6 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 0.011721 0.006767 0.000000 0.00000 SCALE2 0.000000 0.013534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019534 0.00000