HEADER HYDROLASE 18-APR-22 7UPV TITLE STRUCTURE OF MAIZE BZR1-TYPE BETA-AMYLASE PROVIDES NEW INSIGHTS INTO TITLE 2 ITS NONCATALYTIC ADAPTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-AMYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_TAXID: 4577; SOURCE 4 GENE: ZEAMMB73_ZM00001D053975; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GH-14, MAIZE BETA-AMYLASE, BZR1-BAM8, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PALAYAM,F.SUN,N.SHABEK REVDAT 4 18-OCT-23 7UPV 1 REMARK REVDAT 3 31-AUG-22 7UPV 1 JRNL REVDAT 2 24-AUG-22 7UPV 1 JRNL REVDAT 1 17-AUG-22 7UPV 0 JRNL AUTH F.SUN,M.PALAYAM,N.SHABEK JRNL TITL STRUCTURE OF MAIZE BZR1-TYPE BETA-AMYLASE BAM8 PROVIDES NEW JRNL TITL 2 INSIGHTS INTO ITS NONCATALYTIC ADAPTATION. JRNL REF J.STRUCT.BIOL. V. 214 07885 2022 JRNL REFN ESSN 1095-8657 JRNL PMID 35961473 JRNL DOI 10.1016/J.JSB.2022.107885 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 34844 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.710 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 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 44.8300 - 4.4400 1.00 2456 149 0.1599 0.2057 REMARK 3 2 4.4400 - 3.5200 1.00 2403 146 0.1641 0.2052 REMARK 3 3 3.5200 - 3.0800 1.00 2410 145 0.2104 0.2473 REMARK 3 4 3.0800 - 2.8000 1.00 2388 145 0.2217 0.2913 REMARK 3 5 2.7900 - 2.5900 1.00 2369 143 0.2300 0.2852 REMARK 3 6 2.5900 - 2.4400 1.00 2405 146 0.2118 0.2647 REMARK 3 7 2.4400 - 2.3200 1.00 2366 143 0.2245 0.2555 REMARK 3 8 2.3200 - 2.2200 1.00 2381 144 0.2195 0.2596 REMARK 3 9 2.2200 - 2.1300 1.00 2378 145 0.2220 0.2900 REMARK 3 10 2.1300 - 2.0600 0.99 2386 145 0.2310 0.3160 REMARK 3 11 2.0600 - 2.0000 0.99 2370 143 0.2576 0.2899 REMARK 3 12 2.0000 - 1.9400 0.98 2302 141 0.2655 0.3029 REMARK 3 13 1.9400 - 1.8900 0.94 2233 136 0.3070 0.3685 REMARK 3 14 1.8900 - 1.8400 0.84 2006 120 0.3350 0.3641 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.11 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 7UPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5-6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35028 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 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: PHASER REMARK 200 STARTING MODEL: 1BYA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MGCL2, 0.1M SODIUM CITRATE REMARK 280 TRIBASIC DIHYDRATE, 8% POLYETHYLENE GLYCOL 20000, PH 5.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 34.57050 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 GLN A 620 REMARK 465 GLN A 621 REMARK 465 GLN A 622 REMARK 465 GLN A 623 REMARK 465 PRO A 624 REMARK 465 PRO A 625 REMARK 465 LEU A 626 REMARK 465 GLY A 649 REMARK 465 GLU A 650 REMARK 465 GLY A 651 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 THR A 209 152.86 -49.02 REMARK 500 ASP A 233 89.98 -159.48 REMARK 500 GLU A 262 57.58 -103.36 REMARK 500 PHE A 294 31.74 -89.70 REMARK 500 LEU A 347 72.08 -103.81 REMARK 500 CYS A 394 58.78 -119.71 REMARK 500 PRO A 403 42.44 -100.43 REMARK 500 GLN A 409 50.26 -111.35 REMARK 500 ASP A 458 54.59 -112.53 REMARK 500 ARG A 505 47.32 -88.14 REMARK 500 THR A 550 9.69 -66.21 REMARK 500 VAL A 551 -8.25 -59.63 REMARK 500 ASP A 562 80.01 -151.23 REMARK 500 ARG A 590 48.06 -140.25 REMARK 500 ARG A 605 -41.47 78.09 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7UPV A 203 651 UNP A0A1D6QTZ9_MAIZE DBREF2 7UPV A A0A1D6QTZ9 136 584 SEQADV 7UPV MET A 202 UNP A0A1D6QTZ INITIATING METHIONINE SEQRES 1 A 450 MET LEU PHE PRO ASP ASP TYR THR LYS THR PRO TYR ILE SEQRES 2 A 450 PRO VAL TYR ALA SER LEU PRO MET GLY ILE ILE ASN SER SEQRES 3 A 450 HIS CYS GLN LEU VAL ASP PRO GLU SER VAL ARG ALA GLU SEQRES 4 A 450 LEU ARG GLN LEU LYS SER LEU ASN VAL ASP GLY VAL VAL SEQRES 5 A 450 VAL ASP CYS TRP TRP GLY ILE VAL GLU ALA TRP THR PRO SEQRES 6 A 450 ARG LYS TYR GLU TRP SER GLY TYR ARG ASP LEU PHE GLY SEQRES 7 A 450 ILE ILE LYS GLU PHE LYS LEU LYS VAL GLN VAL VAL LEU SEQRES 8 A 450 SER PHE HIS GLY SER GLY GLU THR GLY SER GLY ASP VAL SEQRES 9 A 450 LEU ILE SER LEU PRO LYS TRP ILE MET GLU ILE ALA LYS SEQRES 10 A 450 GLU ASN GLN ASP ILE PHE PHE THR ASP ARG GLU GLY ARG SEQRES 11 A 450 ARG ASN THR GLU CYS LEU SER TRP GLY ILE ASP LYS GLU SEQRES 12 A 450 ARG VAL LEU ARG GLY ARG THR GLY ILE GLU VAL CYS PHE SEQRES 13 A 450 ASP PHE MET ARG SER PHE HIS MET GLU PHE ARG ASN LEU SEQRES 14 A 450 SER GLU GLU GLY LEU VAL SER SER ILE GLU ILE GLY LEU SEQRES 15 A 450 GLY ALA SER GLY GLU LEU ARG TYR PRO SER CYS PRO GLU SEQRES 16 A 450 THR MET GLY TRP LYS TYR PRO GLY ILE GLY GLU PHE GLN SEQRES 17 A 450 CYS TYR ASP ARG TYR MET GLN LYS ASN LEU ARG GLN SER SEQRES 18 A 450 ALA LEU SER ARG GLY HIS LEU PHE TRP ALA ARG GLY PRO SEQRES 19 A 450 ASP ASN ALA GLY TYR TYR ASN SER ARG PRO HIS GLU THR SEQRES 20 A 450 GLY PHE PHE CYS ASP GLY GLY ASP TYR ASP SER TYR TYR SEQRES 21 A 450 GLY ARG PHE PHE LEU ASN TRP TYR SER GLY VAL LEU MET SEQRES 22 A 450 ASP HIS VAL ASP GLN VAL LEU SER LEU ALA THR LEU ALA SEQRES 23 A 450 PHE ASP GLY ALA GLU ILE VAL VAL LYS VAL PRO SER ILE SEQRES 24 A 450 TYR TRP TRP TYR ARG THR ALA SER HIS ALA ALA GLU LEU SEQRES 25 A 450 THR ALA GLY PHE TYR ASN THR THR ASN ARG ASP GLY TYR SEQRES 26 A 450 SER PRO VAL PHE ARG MET LEU LYS LYS HIS SER VAL ILE SEQRES 27 A 450 LEU LYS LEU VAL CYS TYR GLY PRO GLU TYR THR VAL HIS SEQRES 28 A 450 GLU LYS ASP ASP ASP GLU ALA PHE ALA ASP PRO GLU GLY SEQRES 29 A 450 LEU THR TRP GLN VAL ILE ASN ALA ALA TRP ASP GLN GLY SEQRES 30 A 450 LEU PRO LEU CYS ILE GLU SER ALA LEU PRO CYS ARG ASN SEQRES 31 A 450 GLY GLU ALA TYR SER ARG ILE LEU ASP THR ALA LYS PRO SEQRES 32 A 450 ARG ASP ASP PRO ASP ARG HIS HIS ALA ALA SER PHE ALA SEQRES 33 A 450 TYR ARG GLN GLN GLN GLN PRO PRO LEU ARG GLU ALA CYS SEQRES 34 A 450 LEU SER GLU LEU CYS THR PHE VAL LYS CYS MET HIS GLY SEQRES 35 A 450 GLU ALA PRO GLN ASN GLY GLU GLY HET GOL A 701 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *40(H2 O) HELIX 1 AA1 ASP A 233 LEU A 247 1 15 HELIX 2 AA2 TRP A 258 GLU A 262 1 5 HELIX 3 AA3 TRP A 271 PHE A 284 1 14 HELIX 4 AA4 PRO A 310 ASN A 320 1 11 HELIX 5 AA5 TRP A 339 ASP A 342 5 4 HELIX 6 AA6 THR A 351 GLU A 373 1 23 HELIX 7 AA7 ASP A 412 ARG A 426 1 15 HELIX 8 AA8 GLY A 427 ALA A 432 5 6 HELIX 9 AA9 ARG A 444 THR A 448 5 5 HELIX 10 AB1 GLY A 455 ASP A 458 5 4 HELIX 11 AB2 SER A 459 PHE A 488 1 30 HELIX 12 AB3 HIS A 509 GLY A 516 1 8 HELIX 13 AB4 TYR A 526 LYS A 535 1 10 HELIX 14 AB5 TYR A 549 LYS A 554 1 6 HELIX 15 AB6 ASP A 562 GLN A 577 1 16 HELIX 16 AB7 ASN A 591 LYS A 603 1 13 HELIX 17 AB8 GLU A 628 HIS A 642 1 15 SHEET 1 AA1 9 VAL A 216 SER A 219 0 SHEET 2 AA1 9 GLY A 251 TRP A 257 1 O VAL A 253 N ALA A 218 SHEET 3 AA1 9 LYS A 287 SER A 293 1 O VAL A 291 N CYS A 256 SHEET 4 AA1 9 VAL A 376 GLY A 382 1 O GLU A 380 N VAL A 290 SHEET 5 AA1 9 ILE A 493 VAL A 497 1 O VAL A 494 N ILE A 379 SHEET 6 AA1 9 ILE A 539 CYS A 544 1 O ILE A 539 N ILE A 493 SHEET 7 AA1 9 LEU A 581 ALA A 586 1 O CYS A 582 N LEU A 540 SHEET 8 AA1 9 SER A 615 ARG A 619 1 O ALA A 617 N ILE A 583 SHEET 9 AA1 9 VAL A 216 SER A 219 1 N TYR A 217 O PHE A 616 SHEET 1 AA2 2 PHE A 324 THR A 326 0 SHEET 2 AA2 2 ARG A 332 LEU A 337 -1 O ASN A 333 N PHE A 325 SSBOND 1 CYS A 589 CYS A 630 1555 1555 2.04 CISPEP 1 TYR A 402 PRO A 403 0 0.96 CRYST1 50.896 69.141 59.123 90.00 95.04 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 0.019648 0.000000 0.001732 0.00000 SCALE2 0.000000 0.014463 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016979 0.00000