HEADER TRANSFERASE 12-JUL-21 7RE6 TITLE CRYSTAL STRUCTURE OF THE BROWN DOG TICK (RHIPICEPHALUS SANGUINEUS) TITLE 2 ARGININE KINASE IN ABSENCE OF SUBSTRATE OR LIGANDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGININE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.3.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIPICEPHALUS SANGUINEUS; SOURCE 3 ORGANISM_TAXID: 34632; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOTRANSFERASE, MONOMER, PHOSPHAGEN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.C.GOMEZ-YANES,K.D.GARCIA-OROZCO,A.A.LOPEZ-ZAVALA,R.R.SOTELO-MUNDO REVDAT 3 25-OCT-23 7RE6 1 REMARK REVDAT 2 30-NOV-22 7RE6 1 JRNL REVDAT 1 17-NOV-21 7RE6 0 JRNL AUTH A.C.GOMEZ-YANES,E.N.MORENO-CORDOVA,K.D.GARCIA-OROZCO, JRNL AUTH 2 A.LAINO,M.A.ISLAS-OSUNA,A.A.LOPEZ-ZAVALA,J.G.VALENZUELA, JRNL AUTH 3 R.R.SOTELO-MUNDO JRNL TITL THE ARGININE KINASE FROM THE TICK RHIPICEPHALUS SANGUINEUS JRNL TITL 2 IS AN EFFICIENT BIOCATALYST JRNL REF CATALYSTS V. 12 2022 JRNL REFN ESSN 2073-4344 JRNL DOI 10.3390/CATAL12101178 REMARK 2 REMARK 2 RESOLUTION. 1.53 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 52784 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 2530 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 35.8200 - 4.0100 0.98 2913 122 0.1526 0.1888 REMARK 3 2 4.0100 - 3.1800 0.99 2894 111 0.1414 0.1717 REMARK 3 3 3.1800 - 2.7800 1.00 2838 167 0.1525 0.1843 REMARK 3 4 2.7800 - 2.5300 1.00 2878 124 0.1457 0.1499 REMARK 3 5 2.5300 - 2.3400 0.98 2779 154 0.1465 0.1851 REMARK 3 6 2.3400 - 2.2100 0.98 2747 174 0.1481 0.1688 REMARK 3 7 2.2100 - 2.1000 0.98 2800 155 0.1521 0.1726 REMARK 3 8 2.1000 - 2.0000 0.99 2806 147 0.1518 0.2027 REMARK 3 9 2.0000 - 1.9300 0.99 2809 153 0.1574 0.1792 REMARK 3 10 1.9300 - 1.8600 0.99 2822 132 0.1703 0.1915 REMARK 3 11 1.8600 - 1.8000 1.00 2813 158 0.1688 0.2177 REMARK 3 12 1.8000 - 1.7500 0.97 2781 149 0.1784 0.2189 REMARK 3 13 1.7500 - 1.7000 0.97 2754 143 0.1689 0.2150 REMARK 3 14 1.7000 - 1.6600 0.97 2770 130 0.1737 0.1815 REMARK 3 15 1.6600 - 1.6300 0.98 2818 110 0.1858 0.2047 REMARK 3 16 1.6300 - 1.5900 0.98 2799 135 0.1950 0.2417 REMARK 3 17 1.5900 - 1.5600 0.98 2771 143 0.2001 0.2324 REMARK 3 18 1.5600 - 1.5300 0.87 2462 123 0.2305 0.2717 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) : 0.132 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.937 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.24 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 : 0.010 2809 REMARK 3 ANGLE : 1.156 3786 REMARK 3 CHIRALITY : 0.057 416 REMARK 3 PLANARITY : 0.011 491 REMARK 3 DIHEDRAL : 5.556 379 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 7RE6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000256989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.19 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52892 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 35.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 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: PHASER REMARK 200 STARTING MODEL: 4AM1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 25% P/V PEG REMARK 280 3350, PH 7.8, MICROBATCH, TEMPERATURE 289K 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 30.70500 REMARK 290 SMTRY3 2 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 MET A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 LEU A -10 REMARK 465 GLU A -9 REMARK 465 VAL A -8 REMARK 465 LEU A -7 REMARK 465 PHE A -6 REMARK 465 GLN A -5 REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 SER A -2 REMARK 465 GLY A -1 REMARK 465 MET A 0 REMARK 465 ARG A 312 REMARK 465 GLY A 313 REMARK 465 GLU A 314 REMARK 465 HIS A 315 REMARK 465 THR A 316 REMARK 465 GLU A 317 REMARK 465 SER A 318 REMARK 465 GLU A 319 REMARK 465 GLY A 320 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 732 O HOH A 771 2.18 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 VAL A 65 -70.25 -99.10 REMARK 500 ASP A 114 70.39 -154.53 REMARK 500 GLU A 225 -61.64 -158.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RE6 A -17 356 PDB 7RE6 7RE6 -17 356 SEQRES 1 A 374 MET HIS HIS HIS HIS HIS HIS LEU GLU VAL LEU PHE GLN SEQRES 2 A 374 GLY PRO SER GLY MET SER VAL ASP GLN ALA THR LEU ASP SEQRES 3 A 374 LYS LEU GLU ALA GLY PHE LYS LYS LEU GLN ASP ALA LYS SEQRES 4 A 374 ASP CYS LYS SER LEU LEU LYS LYS TYR LEU THR LYS GLU SEQRES 5 A 374 ILE PHE ASP ARG LEU LYS THR ARG LYS THR ALA MET GLY SEQRES 6 A 374 ALA THR LEU LEU ASP VAL ILE GLN SER GLY VAL GLU ASN SEQRES 7 A 374 LEU ASP SER GLY VAL GLY VAL TYR ALA PRO ASP ALA GLU SEQRES 8 A 374 SER TYR THR VAL PHE ALA ASP LEU PHE ASP PRO VAL ILE SEQRES 9 A 374 GLU ASP TYR HIS GLY GLY PHE LYS PRO THR ASP LYS HIS SEQRES 10 A 374 PRO PRO THR ASP PHE GLY ASP MET ASN THR ILE VAL ASN SEQRES 11 A 374 VAL ASP PRO GLU ASN LYS TYR VAL VAL SER THR ARG VAL SEQRES 12 A 374 ARG CYS GLY ARG SER LEU GLN GLY TYR PRO PHE ASN PRO SEQRES 13 A 374 CYS LEU THR GLU ALA GLN TYR LYS GLU MET GLU ASP LYS SEQRES 14 A 374 VAL SER SER GLN LEU LYS GLY MET THR GLY ASP LEU LYS SEQRES 15 A 374 GLY THR TYR TYR PRO LEU THR GLY MET ASP LYS LYS THR SEQRES 16 A 374 GLN GLN GLN LEU ILE ASP ASP HIS PHE LEU PHE LYS GLU SEQRES 17 A 374 GLY ASP ARG PHE LEU GLN ALA ALA ASN ALA CYS ARG TYR SEQRES 18 A 374 TRP PRO THR GLY ARG GLY ILE TYR HIS ASN ASP ALA LYS SEQRES 19 A 374 THR PHE LEU VAL TRP VAL ASN GLU GLU ASP HIS LEU ARG SEQRES 20 A 374 ILE ILE SER MET GLN GLN GLY GLY ASP LEU LYS GLN VAL SEQRES 21 A 374 TYR SER ARG MET VAL SER GLY VAL LYS GLU ILE GLU LYS SEQRES 22 A 374 LYS LEU PRO PHE SER ARG ASP ASP ARG LEU GLY PHE LEU SEQRES 23 A 374 THR PHE CYS PRO THR ASN LEU GLY THR THR ILE ARG ALA SEQRES 24 A 374 SER VAL HIS ILE LYS LEU PRO LYS LEU ALA ALA ASP LYS SEQRES 25 A 374 ALA LYS LEU ASP SER ILE ALA ALA LYS TYR ASN LEU GLN SEQRES 26 A 374 VAL ARG GLY THR ARG GLY GLU HIS THR GLU SER GLU GLY SEQRES 27 A 374 ALA VAL TYR ASP ILE SER ASN LYS ARG ARG MET GLY LEU SEQRES 28 A 374 THR GLU TYR GLN ALA VAL ARG GLU MET GLN ASP GLY ILE SEQRES 29 A 374 GLN GLU LEU ILE LYS LEU GLU GLN ALA ALA FORMUL 2 HOH *377(H2 O) HELIX 1 AA1 ASP A 3 ALA A 20 1 18 HELIX 2 AA2 SER A 25 LEU A 31 1 7 HELIX 3 AA3 THR A 32 LYS A 40 1 9 HELIX 4 AA4 LEU A 50 ASN A 60 1 11 HELIX 5 AA5 GLU A 73 PHE A 78 1 6 HELIX 6 AA6 PHE A 78 HIS A 90 1 13 HELIX 7 AA7 ASP A 106 ILE A 110 5 5 HELIX 8 AA8 THR A 141 GLY A 158 1 18 HELIX 9 AA9 MET A 159 LEU A 163 5 5 HELIX 10 AB1 ASP A 174 ASP A 184 1 11 HELIX 11 AB2 ASP A 192 ALA A 198 1 7 HELIX 12 AB3 ASP A 238 LYS A 255 1 18 HELIX 13 AB4 CYS A 271 LEU A 275 5 5 HELIX 14 AB5 LEU A 287 ALA A 292 1 6 HELIX 15 AB6 ASP A 293 TYR A 304 1 12 HELIX 16 AB7 THR A 334 ALA A 356 1 23 SHEET 1 AA1 8 GLY A 165 PRO A 169 0 SHEET 2 AA1 8 GLY A 209 ASN A 213 -1 O ILE A 210 N TYR A 168 SHEET 3 AA1 8 PHE A 218 VAL A 222 -1 O VAL A 222 N GLY A 209 SHEET 4 AA1 8 LEU A 228 GLN A 235 -1 O ILE A 231 N LEU A 219 SHEET 5 AA1 8 VAL A 120 ARG A 129 -1 N CYS A 127 O ILE A 230 SHEET 6 AA1 8 ARG A 280 LYS A 286 -1 O SER A 282 N ARG A 124 SHEET 7 AA1 8 VAL A 322 ASN A 327 -1 O TYR A 323 N ILE A 285 SHEET 8 AA1 8 LEU A 306 ARG A 309 -1 N GLN A 307 O SER A 326 SHEET 1 AA2 2 ARG A 261 ASP A 262 0 SHEET 2 AA2 2 GLY A 266 PHE A 267 -1 O GLY A 266 N ASP A 262 CISPEP 1 TRP A 204 PRO A 205 0 -0.53 CRYST1 48.412 61.410 61.342 90.00 96.56 90.00 P 1 21 1 2 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 0.020656 0.000000 0.002374 0.00000 SCALE2 0.000000 0.016284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016409 0.00000