HEADER SUGAR BINDING PROTEIN 06-JUL-22 8DKY TITLE CRYSTAL STRUCTURE OF THE AQUIFEX AEOLICUS WZT CARBOHYDRATE BINDING TITLE 2 DOMAIN BOUND TO 3-O-METHYL-D-MANNOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABC TRANSPORTER; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS VF5; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: ABCT4, AQ_1094; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS O ANTIGEN ABC TRANSPORTER, CARBOHYDRATE BINDING DOMAIN, 3-O-METHYL-D- KEYWDS 2 MANNOSE, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.SPELLMON,J.ZIMMER REVDAT 2 18-OCT-23 8DKY 1 REMARK REVDAT 1 21-SEP-22 8DKY 0 JRNL AUTH N.SPELLMON,A.MUSZYNSKI,I.GORNIAK,J.VLACH,D.HAHN,P.AZADI, JRNL AUTH 2 J.ZIMMER JRNL TITL MOLECULAR BASIS FOR POLYSACCHARIDE RECOGNITION AND MODULATED JRNL TITL 2 ATP HYDROLYSIS BY THE O ANTIGEN ABC TRANSPORTER. JRNL REF NAT COMMUN V. 13 5226 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36064941 JRNL DOI 10.1038/S41467-022-32597-2 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 41094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 2126 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 48.6400 - 3.9700 1.00 2803 145 0.2226 0.2602 REMARK 3 2 3.9700 - 3.1500 1.00 2679 139 0.2362 0.2506 REMARK 3 3 3.1500 - 2.7500 0.99 2636 139 0.2662 0.2713 REMARK 3 4 2.7500 - 2.5000 1.00 2621 157 0.2736 0.3072 REMARK 3 5 2.5000 - 2.3200 1.00 2590 136 0.2706 0.2928 REMARK 3 6 2.3200 - 2.1900 1.00 2597 155 0.2625 0.3014 REMARK 3 7 2.1900 - 2.0800 1.00 2616 149 0.2596 0.2926 REMARK 3 8 2.0800 - 1.9900 0.98 2535 132 0.2561 0.2833 REMARK 3 9 1.9900 - 1.9100 0.99 2592 158 0.2656 0.2964 REMARK 3 10 1.9100 - 1.8400 1.00 2577 137 0.2823 0.3051 REMARK 3 11 1.8400 - 1.7900 1.00 2588 138 0.3028 0.3248 REMARK 3 12 1.7900 - 1.7300 1.00 2577 158 0.3071 0.3503 REMARK 3 13 1.7300 - 1.6900 1.00 2597 129 0.3198 0.3456 REMARK 3 14 1.6900 - 1.6500 1.00 2568 126 0.3455 0.3810 REMARK 3 15 1.6500 - 1.6100 0.93 2392 128 0.3936 0.4398 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.35 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8DKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000266871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 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) : 1.0 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 95.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.78200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 6O14 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1M TRICINE PH 8.8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 28.28050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.65800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.08450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.65800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.28050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.08450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL 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 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 LYS A 376 -134.71 -130.96 REMARK 500 GLU B 318 31.73 75.48 REMARK 500 LYS B 376 -140.31 -101.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 8DKY A 254 395 UNP O67181 O67181_AQUAE 255 396 DBREF 8DKY B 254 395 UNP O67181 O67181_AQUAE 255 396 SEQADV 8DKY GLY A 252 UNP O67181 EXPRESSION TAG SEQADV 8DKY SER A 253 UNP O67181 EXPRESSION TAG SEQADV 8DKY GLY B 252 UNP O67181 EXPRESSION TAG SEQADV 8DKY SER B 253 UNP O67181 EXPRESSION TAG SEQRES 1 A 144 GLY SER ASN PHE LYS ALA VAL ILE LYS GLU VAL ARG LEU SEQRES 2 A 144 LYS SER GLU HIS GLY TYR THR ASN ASN PHE PRO SER GLY SEQRES 3 A 144 ASP THR LEU PHE ILE GLU LEU ASP VAL GLU ALA LYS GLU SEQRES 4 A 144 ASP LEU GLN ASP VAL VAL ALA GLY ILE LEU ILE ARG ASP SEQRES 5 A 144 ARG PHE GLY GLN ASP ILE PHE GLY ILE ASN THR TYR LEU SEQRES 6 A 144 MET GLU LYS LYS VAL GLU LEU LYS LYS GLY LYS TYR LEU SEQRES 7 A 144 PHE THR PHE LYS MET PRO LEU ASN LEU ALA PRO GLY LYS SEQRES 8 A 144 TYR THR LEU THR VAL ALA LEU HIS LYS GLY MET ASP HIS SEQRES 9 A 144 ALA GLN GLU CYS TYR HIS TRP ILE ASP ASN VAL CYS ASN SEQRES 10 A 144 PHE GLU VAL ASN GLY PHE LYS LYS GLU GLN PHE VAL GLY SEQRES 11 A 144 VAL CYS TYR LEU PRO THR GLU PHE ASN TYR ARG LYS ILE SEQRES 12 A 144 PRO SEQRES 1 B 144 GLY SER ASN PHE LYS ALA VAL ILE LYS GLU VAL ARG LEU SEQRES 2 B 144 LYS SER GLU HIS GLY TYR THR ASN ASN PHE PRO SER GLY SEQRES 3 B 144 ASP THR LEU PHE ILE GLU LEU ASP VAL GLU ALA LYS GLU SEQRES 4 B 144 ASP LEU GLN ASP VAL VAL ALA GLY ILE LEU ILE ARG ASP SEQRES 5 B 144 ARG PHE GLY GLN ASP ILE PHE GLY ILE ASN THR TYR LEU SEQRES 6 B 144 MET GLU LYS LYS VAL GLU LEU LYS LYS GLY LYS TYR LEU SEQRES 7 B 144 PHE THR PHE LYS MET PRO LEU ASN LEU ALA PRO GLY LYS SEQRES 8 B 144 TYR THR LEU THR VAL ALA LEU HIS LYS GLY MET ASP HIS SEQRES 9 B 144 ALA GLN GLU CYS TYR HIS TRP ILE ASP ASN VAL CYS ASN SEQRES 10 B 144 PHE GLU VAL ASN GLY PHE LYS LYS GLU GLN PHE VAL GLY SEQRES 11 B 144 VAL CYS TYR LEU PRO THR GLU PHE ASN TYR ARG LYS ILE SEQRES 12 B 144 PRO HET U90 A 401 13 HET U90 B 401 13 HETNAM U90 3-O-METHYL-ALPHA-D-MANNOPYRANOSE FORMUL 3 U90 2(C7 H14 O6) FORMUL 5 HOH *149(H2 O) SHEET 1 AA1 4 ALA A 257 LYS A 265 0 SHEET 2 AA1 4 THR A 279 ALA A 288 -1 O GLU A 283 N ARG A 263 SHEET 3 AA1 4 GLY A 326 PRO A 335 -1 O MET A 334 N LEU A 280 SHEET 4 AA1 4 GLU B 388 ILE B 394 -1 O ILE B 394 N LYS A 327 SHEET 1 AA2 5 ASN A 273 SER A 276 0 SHEET 2 AA2 5 GLU A 358 PHE A 374 1 O GLY A 373 N SER A 276 SHEET 3 AA2 5 GLY A 341 LYS A 351 -1 N TYR A 343 O PHE A 369 SHEET 4 AA2 5 VAL A 295 ASP A 303 -1 N VAL A 296 O HIS A 350 SHEET 5 AA2 5 ASP A 308 ASN A 313 -1 O PHE A 310 N ILE A 301 SHEET 1 AA3 4 GLU A 388 ILE A 394 0 SHEET 2 AA3 4 GLY B 326 PRO B 335 -1 O LYS B 327 N ILE A 394 SHEET 3 AA3 4 THR B 279 ALA B 288 -1 N LEU B 280 O MET B 334 SHEET 4 AA3 4 ALA B 257 LYS B 265 -1 N LYS B 260 O ASP B 285 SHEET 1 AA4 5 ASN B 273 SER B 276 0 SHEET 2 AA4 5 GLU B 358 PHE B 374 1 O GLY B 373 N SER B 276 SHEET 3 AA4 5 GLY B 341 LYS B 351 -1 N TYR B 343 O PHE B 369 SHEET 4 AA4 5 LEU B 292 ASP B 303 -1 N VAL B 296 O HIS B 350 SHEET 5 AA4 5 ASP B 308 ASN B 313 -1 O ILE B 309 N ILE B 301 SHEET 1 AA5 5 ASN B 273 SER B 276 0 SHEET 2 AA5 5 GLU B 358 PHE B 374 1 O GLY B 373 N SER B 276 SHEET 3 AA5 5 GLY B 341 LYS B 351 -1 N TYR B 343 O PHE B 369 SHEET 4 AA5 5 LEU B 292 ASP B 303 -1 N VAL B 296 O HIS B 350 SHEET 5 AA5 5 VAL B 321 LEU B 323 -1 O LEU B 323 N LEU B 292 CRYST1 56.561 58.169 95.316 90.00 90.00 90.00 P 21 21 21 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 0.017680 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010491 0.00000