HEADER MOTOR PROTEIN 16-AUG-21 7RTX TITLE ACTOPHORIN GROWN IN MICROGRAVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTOPHORIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACANTHAMOEBA CASTELLANII; SOURCE 3 ORGANISM_COMMON: AMOEBA; SOURCE 4 ORGANISM_TAXID: 5755; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MICROGRAVITY, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.L.LIEBERMAN,S.QUIRK REVDAT 2 18-OCT-23 7RTX 1 REMARK REVDAT 1 22-DEC-21 7RTX 0 JRNL AUTH S.QUIRK,R.L.LIEBERMAN JRNL TITL IMPROVED RESOLUTION CRYSTAL STRUCTURE OF ACANTHAMOEBA JRNL TITL 2 ACTOPHORIN REVEALS STRUCTURAL PLASTICITY NOT INDUCED BY JRNL TITL 3 MICROGRAVITY. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 77 452 2021 JRNL REFN ESSN 2053-230X JRNL PMID 34866600 JRNL DOI 10.1107/S2053230X21011419 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 28851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.280 REMARK 3 FREE R VALUE TEST SET COUNT : 1813 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 34.6600 - 3.8800 0.98 2068 147 0.1531 0.1820 REMARK 3 2 3.8800 - 3.0800 0.96 2029 136 0.1738 0.2010 REMARK 3 3 3.0800 - 2.6900 0.98 2080 140 0.1851 0.2291 REMARK 3 4 2.6900 - 2.4400 0.98 2061 138 0.1989 0.2461 REMARK 3 5 2.4400 - 2.2700 0.96 2059 134 0.1921 0.2100 REMARK 3 6 2.2700 - 2.1400 0.95 2021 130 0.1959 0.2659 REMARK 3 7 2.1300 - 2.0300 0.98 2074 139 0.2052 0.2353 REMARK 3 8 2.0300 - 1.9400 0.99 2113 139 0.2239 0.2814 REMARK 3 9 1.9400 - 1.8700 0.99 2091 143 0.2192 0.2856 REMARK 3 10 1.8700 - 1.8000 0.99 2107 140 0.2370 0.2599 REMARK 3 11 1.8000 - 1.7400 1.00 2105 142 0.2474 0.2927 REMARK 3 12 1.7400 - 1.6900 1.00 2109 146 0.2721 0.3003 REMARK 3 13 1.6900 - 1.6500 1.00 2121 139 0.3337 0.3748 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) : 0.218 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.038 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.09 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 : 0.012 1181 REMARK 3 ANGLE : 1.202 1613 REMARK 3 CHIRALITY : 0.083 173 REMARK 3 PLANARITY : 0.010 220 REMARK 3 DIHEDRAL : 5.744 168 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 2 THROUGH 134) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5995 -3.7596 6.6632 REMARK 3 T TENSOR REMARK 3 T11: 0.1923 T22: 0.1784 REMARK 3 T33: 0.1941 T12: -0.0198 REMARK 3 T13: 0.0489 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 2.3324 L22: 2.3972 REMARK 3 L33: 2.3891 L12: 0.3283 REMARK 3 L13: 0.5520 L23: 0.5738 REMARK 3 S TENSOR REMARK 3 S11: 0.1297 S12: -0.0928 S13: 0.1708 REMARK 3 S21: 0.0982 S22: -0.0610 S23: -0.0050 REMARK 3 S31: -0.1073 S32: -0.1253 S33: -0.0691 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 7RTX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000258991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 34.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07705 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.87450 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: 1AHQ REMARK 200 REMARK 200 REMARK: LONG (1 - 2 MM) RECTANGULAR CUBOIDS WITH THE OTHER REMARK 200 DIMENSIONS ON THE ORDER OF 0.05 - 0.1 MM. CRYSTALS GROW AT ROOM REMARK 200 TEMPERATURE IN 3-5 DAYS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN, 0.1 M MOPS, 16% REMARK 280 POLYETHYLENE GLYCOL (8,000), PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.90500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.65500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.65500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.90500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.90000 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: 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 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 SER A 1 REMARK 465 ASP A 135 REMARK 465 VAL A 136 REMARK 465 LYS A 137 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 238 O HOH A 289 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O LEU A 18 HZ2 LYS A 92 2454 1.26 REMARK 500 O LEU A 18 NZ LYS A 92 2454 1.75 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 GLU A 39 -66.60 -100.59 REMARK 500 LEU A 108 78.12 -101.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RTX A 1 137 UNP P37167 ACTP_ACACA 2 138 SEQRES 1 A 137 SER GLY ILE ALA VAL SER ASP ASP CYS VAL GLN LYS PHE SEQRES 2 A 137 ASN GLU LEU LYS LEU GLY HIS GLN HIS ARG TYR VAL THR SEQRES 3 A 137 PHE LYS MET ASN ALA SER ASN THR GLU VAL VAL VAL GLU SEQRES 4 A 137 HIS VAL GLY GLY PRO ASN ALA THR TYR GLU ASP PHE LYS SEQRES 5 A 137 SER GLN LEU PRO GLU ARG ASP CYS ARG TYR ALA ILE PHE SEQRES 6 A 137 ASP TYR GLU PHE GLN VAL ASP GLY GLY GLN ARG ASN LYS SEQRES 7 A 137 ILE THR PHE ILE LEU TRP ALA PRO ASP SER ALA PRO ILE SEQRES 8 A 137 LYS SER LYS MET MET TYR THR SER THR LYS ASP SER ILE SEQRES 9 A 137 LYS LYS LYS LEU VAL GLY ILE GLN VAL GLU VAL GLN ALA SEQRES 10 A 137 THR ASP ALA ALA GLU ILE SER GLU ASP ALA VAL SER GLU SEQRES 11 A 137 ARG ALA LYS LYS ASP VAL LYS FORMUL 2 HOH *108(H2 O) HELIX 1 AA1 SER A 6 LEU A 18 1 13 HELIX 2 AA2 THR A 47 SER A 53 1 7 HELIX 3 AA3 PRO A 90 LEU A 108 1 19 HELIX 4 AA4 ALA A 120 ILE A 123 5 4 HELIX 5 AA5 SER A 124 LYS A 133 1 10 SHEET 1 AA1 6 ALA A 4 VAL A 5 0 SHEET 2 AA1 6 GLU A 35 GLY A 42 1 O VAL A 36 N ALA A 4 SHEET 3 AA1 6 TYR A 24 MET A 29 -1 N THR A 26 O GLU A 39 SHEET 4 AA1 6 ARG A 61 VAL A 71 -1 O TYR A 62 N PHE A 27 SHEET 5 AA1 6 GLY A 74 TRP A 84 -1 O TRP A 84 N ARG A 61 SHEET 6 AA1 6 VAL A 113 ALA A 117 1 O VAL A 113 N PHE A 81 CRYST1 39.810 45.800 69.310 90.00 90.00 90.00 P 21 21 21 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 0.025119 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014428 0.00000