HEADER CARBOHYDRATE 25-APR-22 7ZOI TITLE CARBOHYDRATE BINDING DOMAIN CBM92-A FROM A MULTI-CATALYTIC GLUCANASE- TITLE 2 CHITINASE FROM CHITINOPHAGA PINENSIS DSM 2588 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSIDE HYDROLASE FAMILY 18; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CBM92-A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHITINOPHAGA PINENSIS DSM 2588; SOURCE 3 ORGANISM_TAXID: 485918; SOURCE 4 GENE: CPIN_2580; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BETA-TREFOIL, CARBOHYDRATE BINDING DOMAIN, BETA-GLYCAN, CARBOHYDRATE EXPDTA X-RAY DIFFRACTION AUTHOR S.MAZURKEWICH,L.S.MCKEE,Z.LU,G.BRANDEN,J.LARSBRINK REVDAT 3 08-MAY-24 7ZOI 1 TITLE COMPND SOURCE JRNL REVDAT 3 2 1 REMARK DBREF SEQADV REVDAT 2 07-FEB-24 7ZOI 1 REMARK REVDAT 1 10-MAY-23 7ZOI 0 JRNL AUTH M.S.HAO,S.MAZURKEWICH,H.LI,A.KVAMMEN,S.SAHA,S.KOSKELA, JRNL AUTH 2 A.R.INMAN,M.NAKAJIMA,N.TANAKA,H.NAKAI,G.BRANDEN,V.BULONE, JRNL AUTH 3 J.LARSBRINK,L.S.MCKEE JRNL TITL STRUCTURAL AND BIOCHEMICAL ANALYSIS OF FAMILY 92 JRNL TITL 2 CARBOHYDRATE-BINDING MODULES UNCOVERS MULTIVALENT BINDING TO JRNL TITL 3 BETA-GLUCANS. JRNL REF NAT COMMUN V. 15 3429 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38653764 JRNL DOI 10.1038/S41467-024-47584-Y REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 13490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1348 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 38.9500 - 3.0200 1.00 1896 207 0.1755 0.2222 REMARK 3 2 3.0200 - 2.4000 1.00 1785 203 0.2141 0.2601 REMARK 3 3 2.4000 - 2.0900 1.00 1754 197 0.2231 0.2755 REMARK 3 4 2.0900 - 1.9000 0.86 1523 170 0.2360 0.2491 REMARK 3 5 1.9000 - 1.7600 0.69 1215 128 0.2247 0.2329 REMARK 3 6 1.7600 - 1.6600 0.58 1013 113 0.2135 0.2534 REMARK 3 7 1.6600 - 1.5800 0.52 897 99 0.2225 0.2488 REMARK 3 8 1.5800 - 1.5100 0.48 827 96 0.2312 0.2938 REMARK 3 9 1.5100 - 1.4500 0.41 707 81 0.2143 0.2370 REMARK 3 10 1.4500 - 1.4000 0.30 525 54 0.2335 0.3872 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) : 0.142 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.60 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 : 0.006 970 REMARK 3 ANGLE : 0.876 1318 REMARK 3 CHIRALITY : 0.079 135 REMARK 3 PLANARITY : 0.005 175 REMARK 3 DIHEDRAL : 20.698 333 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 7ZOI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.991874 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 : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13501 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 38.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.71000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: 7ZOH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 17.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5 WITH 10 % W/V REMARK 280 PEG 3350, 400 MM NH4SO4, AND 10 MM UREA, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 15.82950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.27800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.85600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.27800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.82950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.85600 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 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 434 REMARK 465 ALA A 435 REMARK 465 SER A 436 REMARK 465 MET A 437 REMARK 465 THR A 438 REMARK 465 GLY A 439 REMARK 465 GLY A 440 REMARK 465 GLN A 441 REMARK 465 GLN A 442 REMARK 465 MET A 443 REMARK 465 GLY A 444 REMARK 465 ARG A 445 REMARK 465 GLY A 446 REMARK 465 SER A 447 REMARK 465 VAL A 448 REMARK 465 GLY A 449 REMARK 465 GLY A 574 REMARK 465 ASN A 575 REMARK 465 ALA A 576 REMARK 465 LEU A 577 REMARK 465 GLU A 578 REMARK 465 HIS A 579 REMARK 465 HIS A 580 REMARK 465 HIS A 581 REMARK 465 HIS A 582 REMARK 465 HIS A 583 REMARK 465 HIS A 584 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 465 19.29 58.43 REMARK 500 CYS A 473 75.38 -100.85 REMARK 500 GLN A 479 -144.61 -125.75 REMARK 500 ASN A 508 15.23 57.46 REMARK 500 ASN A 542 0.21 -66.20 REMARK 500 SER A 563 -153.14 -125.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ZOH RELATED DB: PDB REMARK 900 RELATED ID: 7ZON RELATED DB: PDB REMARK 900 RELATED ID: 7ZOP RELATED DB: PDB REMARK 900 RELATED ID: 7ZOO RELATED DB: PDB DBREF1 7ZOI A 448 576 UNP A0A979GQH9_CHIPD DBREF2 7ZOI A A0A979GQH9 448 576 SEQADV 7ZOI MET A 434 UNP A0A979GQH INITIATING METHIONINE SEQADV 7ZOI ALA A 435 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI SER A 436 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI MET A 437 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI THR A 438 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI GLY A 439 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI GLY A 440 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI GLN A 441 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI GLN A 442 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI MET A 443 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI GLY A 444 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI ARG A 445 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI GLY A 446 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI SER A 447 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI LEU A 577 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI GLU A 578 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI HIS A 579 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI HIS A 580 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI HIS A 581 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI HIS A 582 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI HIS A 583 UNP A0A979GQH EXPRESSION TAG SEQADV 7ZOI HIS A 584 UNP A0A979GQH EXPRESSION TAG SEQRES 1 A 151 MET ALA SER MET THR GLY GLY GLN GLN MET GLY ARG GLY SEQRES 2 A 151 SER VAL GLY LYS THR ILE TRP LEU GLN GLY PHE ASN ASN SEQRES 3 A 151 LYS TYR VAL ASN SER LYS ASN GLY GLN GLY ALA MET TRP SEQRES 4 A 151 CYS ASP SER ASP ALA PRO GLN ALA TRP GLU LEU PHE THR SEQRES 5 A 151 VAL VAL ASP ALA GLY ASN GLY LYS ILE ALA LEU ARG GLY SEQRES 6 A 151 ASN ASN GLY MET TYR VAL SER SER GLU ASN GLY GLU GLN SEQRES 7 A 151 ALA ILE THR CYS ASN ARG PRO ALA ILE GLN GLY TRP GLU SEQRES 8 A 151 ALA PHE ASP TRP LEU GLU THR ALA ASP GLY LYS VAL SER SEQRES 9 A 151 LEU ARG GLY SER ASN GLY LEU PHE ILE SER SER GLU ASN SEQRES 10 A 151 GLY ALA ALA ALA MET THR CYS THR ARG PRO THR ALA SER SEQRES 11 A 151 GLY TRP GLU ALA PHE GLY TYR SER VAL VAL GLY ASN ALA SEQRES 12 A 151 LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *51(H2 O) HELIX 1 AA1 SER A 464 GLN A 468 5 5 HELIX 2 AA2 GLN A 479 LEU A 483 5 5 HELIX 3 AA3 SER A 506 GLU A 510 5 5 HELIX 4 AA4 SER A 548 ALA A 552 5 5 HELIX 5 AA5 SER A 563 ALA A 567 5 5 SHEET 1 AA1 3 THR A 451 ILE A 452 0 SHEET 2 AA1 3 PHE A 484 GLY A 490 -1 O PHE A 484 N ILE A 452 SHEET 3 AA1 3 LYS A 493 ARG A 497 -1 O ALA A 495 N VAL A 487 SHEET 1 AA2 2 TYR A 461 ASN A 463 0 SHEET 2 AA2 2 TRP A 472 SER A 475 -1 O TRP A 472 N ASN A 463 SHEET 1 AA3 2 TYR A 503 SER A 505 0 SHEET 2 AA3 2 THR A 514 ARG A 517 -1 O ARG A 517 N TYR A 503 SHEET 1 AA4 2 ASP A 527 GLU A 530 0 SHEET 2 AA4 2 VAL A 536 ARG A 539 -1 O SER A 537 N LEU A 529 SHEET 1 AA5 2 PHE A 545 SER A 547 0 SHEET 2 AA5 2 THR A 556 ARG A 559 -1 O ARG A 559 N PHE A 545 CRYST1 31.659 53.712 56.556 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 0.031587 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017682 0.00000