HEADER HYDROLASE 08-SEP-20 7CZJ TITLE THE CRYSTAL STRUCTURE OF FAMILY 20 CBM OF MALTOTETRAOSE-FORMING TITLE 2 AMYLASE FROM PSEUDOMONAS SACCHAROPHILA STB07 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCAN 1,4-ALPHA-MALTOTETRAOHYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: G4-AMYLASE,EXO-MALTOTETRAOHYDROLASE,MALTOTETRAOSE-FORMING COMPND 5 AMYLASE,MALTOTETRAOSE-FORMING EXO-AMYLASE; COMPND 6 EC: 3.2.1.60; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PELOMONAS SACCHAROPHILA; SOURCE 3 ORGANISM_TAXID: 304; SOURCE 4 STRAIN: STB07; SOURCE 5 GENE: MTA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FAMILY 20 CBM, MALTOTETRAOSE-FORMING AMYLASE, RECOMBINATION, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.F.LI,X.F.BAN,Z.Q.ZHANG,C.M.LI REVDAT 3 23-OCT-24 7CZJ 1 REMARK REVDAT 2 29-NOV-23 7CZJ 1 REMARK REVDAT 1 08-SEP-21 7CZJ 0 JRNL AUTH Z.Q.ZHANG,X.F.BAN,C.M.LI,Z.B.GU,Y.HONG,L.CHENG,Z.F.LI JRNL TITL THE CRYSTAL STRUCTURE OF FAMILY 20 CBM OF JRNL TITL 2 MALTOTETRAOSE-FORMING AMYLASE FROM PSEUDOMONAS SACCHAROPHILA JRNL TITL 3 STB07 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 48893 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.853 REMARK 3 FREE R VALUE TEST SET COUNT : 2373 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 19.7440 - 6.6480 0.95 585 32 0.2015 0.5490 REMARK 3 2 6.6480 - 4.7150 1.00 1026 56 0.5560 0.6460 REMARK 3 3 4.7150 - 3.8540 1.00 1310 60 0.1723 0.5300 REMARK 3 4 3.8540 - 3.3390 1.00 1509 73 0.5290 0.5670 REMARK 3 5 3.3390 - 2.9880 1.00 1701 82 0.5490 0.5740 REMARK 3 6 2.9880 - 2.7280 1.00 1866 96 0.5410 0.5480 REMARK 3 7 2.7280 - 2.5260 1.00 2015 99 0.1986 0.5520 REMARK 3 8 2.5260 - 2.3630 1.00 2171 107 0.1803 0.5390 REMARK 3 9 2.3630 - 2.2280 1.00 2307 108 0.1769 0.5110 REMARK 3 10 2.2280 - 2.1140 1.00 2432 119 0.5350 0.5530 REMARK 3 11 2.1140 - 2.0160 1.00 2526 133 0.4980 0.5580 REMARK 3 12 2.0160 - 1.9300 1.00 2648 140 0.5170 0.5390 REMARK 3 13 1.9300 - 1.8540 1.00 2772 135 0.1791 0.5600 REMARK 3 14 1.8540 - 1.7870 1.00 2869 143 0.5660 0.5730 REMARK 3 15 1.7870 - 1.7260 1.00 2975 144 0.1723 0.5680 REMARK 3 16 1.7260 - 1.6720 1.00 3027 168 0.5520 0.5940 REMARK 3 17 1.6720 - 1.6220 1.00 3144 160 0.4750 0.5850 REMARK 3 18 1.6220 - 1.5760 1.00 3227 192 0.4700 0.5690 REMARK 3 19 1.5760 - 1.5340 1.00 3346 163 0.5480 0.5870 REMARK 3 20 1.5340 - 1.4950 0.90 3064 163 0.2015 0.5770 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : 0.44600 REMARK 3 B33 (A**2) : -0.31600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 7CZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300017578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978910 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48893 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.495 REMARK 200 RESOLUTION RANGE LOW (A) : 19.743 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: 2Z0B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC DEHYDRATE. 1.0 M LITHIUM SULFATE MONOHYDRATE, REMARK 280 PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 20.20650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.32750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.94150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.32750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.20650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.94150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 DBREF 7CZJ A 1 97 UNP P22963 AMT4_PELSC 455 551 DBREF 7CZJ B 1 97 UNP P22963 AMT4_PELSC 455 551 SEQRES 1 A 97 VAL ASN VAL ASN PHE ARG CYS ASP ASN GLY VAL THR GLN SEQRES 2 A 97 MET GLY ASP SER VAL TYR ALA VAL GLY ASN VAL SER GLN SEQRES 3 A 97 LEU GLY ASN TRP SER PRO ALA SER ALA VAL ARG LEU THR SEQRES 4 A 97 ASP THR SER SER TYR PRO THR TRP LYS GLY SER ILE ALA SEQRES 5 A 97 LEU PRO ASP GLY GLN ASN VAL GLU TRP LYS CYS LEU ILE SEQRES 6 A 97 ARG ASN GLU ALA ASP ALA THR LEU VAL ARG GLN TRP GLN SEQRES 7 A 97 SER GLY GLY ASN ASN GLN VAL GLN ALA ALA ALA GLY ALA SEQRES 8 A 97 SER THR SER GLY SER PHE SEQRES 1 B 97 VAL ASN VAL ASN PHE ARG CYS ASP ASN GLY VAL THR GLN SEQRES 2 B 97 MET GLY ASP SER VAL TYR ALA VAL GLY ASN VAL SER GLN SEQRES 3 B 97 LEU GLY ASN TRP SER PRO ALA SER ALA VAL ARG LEU THR SEQRES 4 B 97 ASP THR SER SER TYR PRO THR TRP LYS GLY SER ILE ALA SEQRES 5 B 97 LEU PRO ASP GLY GLN ASN VAL GLU TRP LYS CYS LEU ILE SEQRES 6 B 97 ARG ASN GLU ALA ASP ALA THR LEU VAL ARG GLN TRP GLN SEQRES 7 B 97 SER GLY GLY ASN ASN GLN VAL GLN ALA ALA ALA GLY ALA SEQRES 8 B 97 SER THR SER GLY SER PHE HET SO4 A 101 5 HET SO4 B 101 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *285(H2 O) HELIX 1 AA1 VAL A 24 ALA A 35 5 12 HELIX 2 AA2 VAL B 24 GLY B 28 5 5 HELIX 3 AA3 SER B 31 ALA B 35 5 5 SHEET 1 AA1 4 ASP A 40 SER A 43 0 SHEET 2 AA1 4 THR A 46 ALA A 52 -1 O LYS A 48 N ASP A 40 SHEET 3 AA1 4 ASN A 2 ASP A 8 -1 N PHE A 5 O GLY A 49 SHEET 4 AA1 4 SER A 92 SER A 96 1 O GLY A 95 N ASP A 8 SHEET 1 AA2 4 VAL A 36 ARG A 37 0 SHEET 2 AA2 4 ASP A 16 GLY A 22 -1 N ALA A 20 O VAL A 36 SHEET 3 AA2 4 ASN A 58 ASN A 67 -1 O LYS A 62 N VAL A 21 SHEET 4 AA2 4 VAL A 74 TRP A 77 -1 O GLN A 76 N ILE A 65 SHEET 1 AA3 4 VAL A 36 ARG A 37 0 SHEET 2 AA3 4 ASP A 16 GLY A 22 -1 N ALA A 20 O VAL A 36 SHEET 3 AA3 4 ASN A 58 ASN A 67 -1 O LYS A 62 N VAL A 21 SHEET 4 AA3 4 ASN A 83 GLN A 86 -1 O VAL A 85 N VAL A 59 SHEET 1 AA4 4 ASP B 40 SER B 43 0 SHEET 2 AA4 4 THR B 46 ALA B 52 -1 O LYS B 48 N ASP B 40 SHEET 3 AA4 4 ASN B 2 ASP B 8 -1 N PHE B 5 O GLY B 49 SHEET 4 AA4 4 SER B 92 SER B 96 1 O GLY B 95 N ASP B 8 SHEET 1 AA5 4 VAL B 36 ARG B 37 0 SHEET 2 AA5 4 ASP B 16 GLY B 22 -1 N ALA B 20 O VAL B 36 SHEET 3 AA5 4 ASN B 58 ASN B 67 -1 O LEU B 64 N TYR B 19 SHEET 4 AA5 4 VAL B 74 TRP B 77 -1 O GLN B 76 N ILE B 65 SHEET 1 AA6 4 VAL B 36 ARG B 37 0 SHEET 2 AA6 4 ASP B 16 GLY B 22 -1 N ALA B 20 O VAL B 36 SHEET 3 AA6 4 ASN B 58 ASN B 67 -1 O LEU B 64 N TYR B 19 SHEET 4 AA6 4 ASN B 83 GLN B 86 -1 O ASN B 83 N TRP B 61 SSBOND 1 CYS A 7 CYS A 63 1555 1555 2.10 SSBOND 2 CYS B 7 CYS B 63 1555 1555 2.08 CISPEP 1 TYR A 44 PRO A 45 0 8.90 CISPEP 2 TYR B 44 PRO B 45 0 7.72 CRYST1 40.413 79.883 92.655 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 0.024745 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010793 0.00000