HEADER HYDROLASE 03-JUL-17 5XXA TITLE BETA-1,4-MANNANASE-SEMET-RMMAN134A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-MANNANASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 20-181; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOPUS MICROSPORUS; SOURCE 3 ORGANISM_TAXID: 58291; SOURCE 4 GENE: BCV71DRAFT_26579, RMCBS344292_04886; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTOCOLSELENO-METHIONINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.Q.JIANG,X.YOU,D.YANG,P.HUANG REVDAT 1 25-JUL-18 5XXA 0 JRNL AUTH Z.Q.JIANG,X.YOU,D.YANG,P.HUANG JRNL TITL STRUCTURE OF ENDO-1,4-BETA-MANNANASE AT 1.76 ANGSTROMS JRNL TITL 2 RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 36267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL 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) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 5XXA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-16 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36268 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 42.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 27.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, TRI-SODIUM CITRATE, VAPOR REMARK 280 DIFFUSION, 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 24.80700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.11550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.54150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.11550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.80700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.54150 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 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 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 ALA A 1 REMARK 465 ASP A 2 REMARK 465 ARG A 3 REMARK 465 ASP A 158 REMARK 465 VAL A 159 REMARK 465 THR A 160 REMARK 465 ALA A 161 REMARK 465 ILE A 162 REMARK 465 ALA B 1 REMARK 465 ASP B 2 REMARK 465 ARG B 3 REMARK 465 ASP B 158 REMARK 465 VAL B 159 REMARK 465 THR B 160 REMARK 465 ALA B 161 REMARK 465 ILE B 162 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 205 O HOH A 283 2.02 REMARK 500 O HOH A 366 O HOH A 378 2.04 REMARK 500 O HOH A 369 O HOH A 374 2.04 REMARK 500 O HOH A 366 O HOH A 375 2.09 REMARK 500 O HOH A 375 O HOH A 378 2.13 REMARK 500 O HOH A 205 O HOH A 246 2.16 REMARK 500 N GLY A 4 O HOH A 201 2.19 REMARK 500 O HOH B 384 O HOH B 385 2.19 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 TYR A 50 -136.08 54.28 REMARK 500 SER A 68 14.22 -148.72 REMARK 500 ASN A 122 98.52 -169.44 REMARK 500 TYR B 50 -135.73 57.94 REMARK 500 SER B 68 12.20 -147.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 384 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH B 385 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH B 386 DISTANCE = 8.65 ANGSTROMS DBREF1 5XXA A 1 162 UNP A0A0A1NDE2_9FUNG DBREF2 5XXA A A0A0A1NDE2 20 181 DBREF1 5XXA B 1 162 UNP A0A0A1NDE2_9FUNG DBREF2 5XXA B A0A0A1NDE2 20 181 SEQRES 1 A 162 ALA ASP ARG GLY THR GLU THR VAL PRO GLY LEU GLY GLN SEQRES 2 A 162 ARG LYS GLN GLN ILE LEU ASN SER GLY GLY GLY VAL TRP SEQRES 3 A 162 ASP LEU ALA ILE ALA MSE LEU GLU THR LYS ASN LEU GLY SEQRES 4 A 162 THR ASP TYR VAL TYR GLY ASP GLY LYS THR TYR ASP SER SEQRES 5 A 162 ALA ASN PHE GLY ILE PHE LYS GLN ASN TRP PHE MSE LEU SEQRES 6 A 162 ARG THR SER THR SER GLN PHE LYS GLY GLN THR THR ASN SEQRES 7 A 162 GLN TRP ASN ASN GLY ALA VAL LEU ASN SER ASN LEU GLN SEQRES 8 A 162 GLN ASP ILE LYS ALA ARG GLN GLU SER GLN ASN TYR TYR SEQRES 9 A 162 GLY PRO ASP LYS TRP PHE ALA GLY HIS ARG ASN GLY GLU SEQRES 10 A 162 SER GLY LEU SER ASN PRO TYR THR GLN ASP ILE THR ASN SEQRES 11 A 162 TYR LYS ASP ALA VAL ASN TRP ILE HIS ASP GLN LEU ALA SEQRES 12 A 162 SER ASP PRO LYS TYR LEU SER ASP ASP THR ARG PHE TRP SEQRES 13 A 162 VAL ASP VAL THR ALA ILE SEQRES 1 B 162 ALA ASP ARG GLY THR GLU THR VAL PRO GLY LEU GLY GLN SEQRES 2 B 162 ARG LYS GLN GLN ILE LEU ASN SER GLY GLY GLY VAL TRP SEQRES 3 B 162 ASP LEU ALA ILE ALA MSE LEU GLU THR LYS ASN LEU GLY SEQRES 4 B 162 THR ASP TYR VAL TYR GLY ASP GLY LYS THR TYR ASP SER SEQRES 5 B 162 ALA ASN PHE GLY ILE PHE LYS GLN ASN TRP PHE MSE LEU SEQRES 6 B 162 ARG THR SER THR SER GLN PHE LYS GLY GLN THR THR ASN SEQRES 7 B 162 GLN TRP ASN ASN GLY ALA VAL LEU ASN SER ASN LEU GLN SEQRES 8 B 162 GLN ASP ILE LYS ALA ARG GLN GLU SER GLN ASN TYR TYR SEQRES 9 B 162 GLY PRO ASP LYS TRP PHE ALA GLY HIS ARG ASN GLY GLU SEQRES 10 B 162 SER GLY LEU SER ASN PRO TYR THR GLN ASP ILE THR ASN SEQRES 11 B 162 TYR LYS ASP ALA VAL ASN TRP ILE HIS ASP GLN LEU ALA SEQRES 12 B 162 SER ASP PRO LYS TYR LEU SER ASP ASP THR ARG PHE TRP SEQRES 13 B 162 VAL ASP VAL THR ALA ILE MODRES 5XXA MSE A 32 MET MODIFIED RESIDUE MODRES 5XXA MSE A 64 MET MODIFIED RESIDUE MODRES 5XXA MSE B 32 MET MODIFIED RESIDUE MODRES 5XXA MSE B 64 MET MODIFIED RESIDUE HET MSE A 32 8 HET MSE A 64 8 HET MSE B 32 8 HET MSE B 64 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *417(H2 O) HELIX 1 AA1 GLY A 10 SER A 21 1 12 HELIX 2 AA2 GLY A 24 THR A 35 1 12 HELIX 3 AA3 VAL A 43 LYS A 48 5 6 HELIX 4 AA4 THR A 49 SER A 52 5 4 HELIX 5 AA5 TRP A 62 THR A 69 1 8 HELIX 6 AA6 THR A 76 SER A 88 5 13 HELIX 7 AA7 ASN A 89 GLY A 105 1 17 HELIX 8 AA8 GLY A 105 SER A 121 1 17 HELIX 9 AA9 THR A 125 ASP A 145 1 21 HELIX 10 AB1 PRO A 146 SER A 150 5 5 HELIX 11 AB2 GLY B 10 ASN B 20 1 11 HELIX 12 AB3 GLY B 24 THR B 35 1 12 HELIX 13 AB4 VAL B 43 LYS B 48 5 6 HELIX 14 AB5 THR B 49 SER B 52 5 4 HELIX 15 AB6 TRP B 62 THR B 69 1 8 HELIX 16 AB7 THR B 76 SER B 88 5 13 HELIX 17 AB8 ASN B 89 GLY B 105 1 17 HELIX 18 AB9 GLY B 105 ASN B 122 1 18 HELIX 19 AC1 THR B 125 SER B 144 1 20 HELIX 20 AC2 ASP B 145 SER B 150 5 6 SHEET 1 AA1 2 THR A 5 THR A 7 0 SHEET 2 AA1 2 THR A 153 PHE A 155 -1 O ARG A 154 N GLU A 6 SHEET 1 AA2 2 ASN A 54 PHE A 55 0 SHEET 2 AA2 2 GLN A 60 ASN A 61 -1 O GLN A 60 N PHE A 55 SHEET 1 AA3 2 THR B 5 THR B 7 0 SHEET 2 AA3 2 THR B 153 PHE B 155 -1 O ARG B 154 N GLU B 6 SHEET 1 AA4 2 ASN B 54 PHE B 55 0 SHEET 2 AA4 2 GLN B 60 ASN B 61 -1 O GLN B 60 N PHE B 55 LINK C ALA A 31 N MSE A 32 1555 1555 1.33 LINK C MSE A 32 N LEU A 33 1555 1555 1.33 LINK C PHE A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N LEU A 65 1555 1555 1.33 LINK C ALA B 31 N MSE B 32 1555 1555 1.32 LINK C MSE B 32 N LEU B 33 1555 1555 1.34 LINK C PHE B 63 N MSE B 64 1555 1555 1.33 LINK C MSE B 64 N LEU B 65 1555 1555 1.33 CRYST1 49.614 59.083 124.231 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 0.020156 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016925 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008050 0.00000