HEADER HYDROLASE 18-AUG-19 6KQT TITLE CRYSTAL STRUCTURE OF GH136 LACTO-N-BIOSIDASE FROM EUBACTERIUM RAMULUS TITLE 2 - NATIVE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTO-N-BIOSIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EUBACTERIUM RAMULUS ATCC 29099; SOURCE 3 ORGANISM_TAXID: 1256908; SOURCE 4 GENE: HMPREF0373_02965; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DELTA-LACZ (DE3)/PRARE2; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS BETA HELIX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.YAMADA,T.ARAKAWA,M.J.PICHLER,M.ABOU HACHEM,S.FUSHINOBU REVDAT 4 27-MAR-24 6KQT 1 HETSYN REVDAT 3 29-JUL-20 6KQT 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 15-JUL-20 6KQT 1 JRNL REVDAT 1 10-JUN-20 6KQT 0 JRNL AUTH M.J.PICHLER,C.YAMADA,B.SHUOKER,C.ALVAREZ-SILVA,A.GOTOH, JRNL AUTH 2 M.L.LETH,E.SCHOOF,T.KATOH,M.SAKANAKA,T.KATAYAMA,C.JIN, JRNL AUTH 3 N.G.KARLSSON,M.ARUMUGAM,S.FUSHINOBU,M.ABOU HACHEM JRNL TITL BUTYRATE PRODUCING COLONIC CLOSTRIDIALES METABOLISE HUMAN JRNL TITL 2 MILK OLIGOSACCHARIDES AND CROSS FEED ON MUCIN VIA CONSERVED JRNL TITL 3 PATHWAYS. JRNL REF NAT COMMUN V. 11 3285 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32620774 JRNL DOI 10.1038/S41467-020-17075-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.PICHLER,C.YAMADA,B.SHUOKER,C.ALVAREZ-SILVA,A.GOTOH, REMARK 1 AUTH 2 M.LETH,E.SCHOOF,T.KATOH,M.SAKANAKA,T.KATAYAMA,C.JIN, REMARK 1 AUTH 3 N.G.KARLSSON,M.ARUMUGAM,S.FUSHINOBU,M.ABOU HACHEM REMARK 1 TITL BUTYRATE PRODUCING CLOSTRIDIALES UTILIZE DISTINCT HUMAN MILK REMARK 1 TITL 2 OLIGOSACCHARIDES CORRELATING TO EARLY COLONIZATION AND REMARK 1 TITL 3 PREVALENCE IN THE HUMAN GUT REMARK 1 REF NAT COMMUN 2020 REMARK 1 REFN ESSN 2041-1723 REMARK 1 DOI 10.1101/2020.04.15.038927 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 53440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2851 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3895 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.1800 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5019 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 706 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.027 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5210 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4514 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7065 ; 1.630 ; 1.649 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10499 ; 1.436 ; 1.584 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 626 ; 7.580 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 320 ;34.431 ;23.281 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 846 ;12.827 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;15.750 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 642 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5957 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1147 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6KQT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-18 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL 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-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56318 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.23300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 1.06500 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.1 M SODIUM CITRATE (PH REMARK 280 5.6), 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.40000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.80000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 54.80000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.40000 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 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 901 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1419 LIES ON A SPECIAL POSITION. 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 GLY A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 LYS A 3 REMARK 465 LEU A 4 REMARK 465 CYS A 5 REMARK 465 GLU A 6 REMARK 465 HIS A 180 REMARK 465 LEU A 181 REMARK 465 ASN A 182 REMARK 465 GLU A 183 REMARK 465 THR A 184 REMARK 465 THR A 185 REMARK 465 VAL A 186 REMARK 465 ASN A 187 REMARK 465 GLU A 188 REMARK 465 ILE A 189 REMARK 465 SER A 190 REMARK 465 ALA A 191 REMARK 465 GLN A 192 REMARK 465 ASP A 193 REMARK 465 VAL A 194 REMARK 465 SER A 195 REMARK 465 ASP A 196 REMARK 465 GLU A 197 REMARK 465 LYS A 198 REMARK 465 SER A 199 REMARK 465 GLU A 224 REMARK 465 ASP A 225 REMARK 465 LYS A 226 REMARK 465 SER A 227 REMARK 465 CYS A 228 REMARK 465 PRO A 229 REMARK 465 GLU A 230 REMARK 465 GLU A 231 REMARK 465 THR A 232 REMARK 465 LYS A 233 REMARK 465 SER A 234 REMARK 465 GLU A 235 REMARK 465 SER A 236 REMARK 465 SER A 237 REMARK 465 ILE A 238 REMARK 465 GLY A 239 REMARK 465 ASN A 240 REMARK 465 CYS A 241 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 874 O HOH A 1396 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 600 CD GLU A 600 OE1 0.075 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 PHE A 58 -18.87 -143.39 REMARK 500 ARG A 144 -168.65 -100.30 REMARK 500 GLN A 320 71.70 -105.99 REMARK 500 GLN A 324 -159.83 -89.99 REMARK 500 ASN A 367 72.91 -150.03 REMARK 500 LYS A 392 -63.73 -145.47 REMARK 500 ALA A 433 86.74 -151.79 REMARK 500 ASN A 444 65.98 61.05 REMARK 500 MET A 472 44.66 -92.94 REMARK 500 ALA A 474 -72.40 -67.23 REMARK 500 GLU A 535 -125.78 58.86 REMARK 500 ALA A 538 -140.88 45.56 REMARK 500 ASP A 568 -101.87 -92.14 REMARK 500 LEU A 599 -172.67 65.19 REMARK 500 SER A 621 76.20 -118.44 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 A1504 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1505 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A1506 DISTANCE = 7.24 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 394 O REMARK 620 2 THR A 396 O 93.3 REMARK 620 3 HOH A 879 O 83.4 100.2 REMARK 620 4 HOH A1195 O 101.4 104.4 154.6 REMARK 620 5 HOH A1326 O 87.4 172.0 87.8 67.7 REMARK 620 N 1 2 3 4 DBREF 6KQT A 1 663 UNP U2PDT9 U2PDT9_EUBRA 1 663 SEQADV 6KQT GLY A -1 UNP U2PDT9 EXPRESSION TAG SEQADV 6KQT ALA A 0 UNP U2PDT9 EXPRESSION TAG SEQRES 1 A 665 GLY ALA MET GLY LYS LEU CYS GLU ASN GLN GLN GLU ILE SEQRES 2 A 665 TYR ALA ALA TYR ARG VAL ALA ASN LEU LEU GLY VAL TYR SEQRES 3 A 665 GLU ASP CYS SER PRO ASN GLY PHE TYR GLN ARG TRP LYS SEQRES 4 A 665 GLN LYS ASN ALA PHE MET LYS ALA GLN ALA GLU GLU PHE SEQRES 5 A 665 GLY ILE GLY SER THR ASP HIS PHE ILE ASP ASP VAL GLU SEQRES 6 A 665 ARG ILE VAL ASP GLN ARG ARG ALA GLU THR GLU TRP LYS SEQRES 7 A 665 ASN ALA ASP ALA TRP LYS ASN GLY THR ALA ALA PHE GLY SEQRES 8 A 665 ALA ARG TYR LEU THR PRO GLU MET TYR LEU ASP TYR GLU SEQRES 9 A 665 LEU LYS SER ILE GLN LEU ALA PHE ALA THR TYR LYS GLY SEQRES 10 A 665 GLU LEU VAL GLY ASN HIS LYS CYS HIS VAL TYR THR GLU SEQRES 11 A 665 ASP GLU LYS ARG ALA PHE TYR ASP ALA ASN GLN ASP LEU SEQRES 12 A 665 PHE THR ARG TYR HIS GLY ASP LEU PHE SER TYR GLU GLU SEQRES 13 A 665 VAL ASP LEU ILE ILE GLU LYS TRP LEU LYS VAL GLN GLU SEQRES 14 A 665 TYR GLN ASP ILE ILE GLU SER VAL VAL ALA ASN THR HIS SEQRES 15 A 665 LEU ASN GLU THR THR VAL ASN GLU ILE SER ALA GLN ASP SEQRES 16 A 665 VAL SER ASP GLU LYS SER ASP ASN ALA VAL ARG TRP ILE SEQRES 17 A 665 THR GLU PHE GLU LYS ILE TRP ASN GLN MET GLN GLU GLU SEQRES 18 A 665 LYS ARG LEU ARG GLU ASP LYS SER CYS PRO GLU GLU THR SEQRES 19 A 665 LYS SER GLU SER SER ILE GLY ASN CYS GLY HIS CYS TYR SEQRES 20 A 665 TYR VAL SER SER ILE HIS GLY ASP ASP ALA ASN ASP GLY SEQRES 21 A 665 THR GLU ASP GLN PRO LEU LYS SER LEU TYR ALA VAL ASN SEQRES 22 A 665 ARG LEU ASP LEU GLN PRO GLY ASP GLN VAL LEU LEU GLU SEQRES 23 A 665 ARG GLY SER VAL PHE GLU ASN GLN PHE LEU HIS LEU ASN SEQRES 24 A 665 VAL GLN GLY THR LYS GLU GLN PRO ILE TYR ILE GLY ALA SEQRES 25 A 665 TYR GLY ASN GLY ALA LYS PRO LEU ILE GLN THR ASN GLY SEQRES 26 A 665 GLN GLY ILE TRP TYR GLN ASP TYR GLY ASN GLU LEU ASP SEQRES 27 A 665 ALA PRO THR HIS VAL TYR ARG GLY TYR VAL SER SER ALA SEQRES 28 A 665 VAL LEU LEU TYR ASP CYS GLU TYR LEU THR VAL GLU ASN SEQRES 29 A 665 LEU GLU ILE SER ASN LYS GLY GLY VAL PHE GLY GLU THR SEQRES 30 A 665 TYR SER ALA PRO HIS LYS MET ASN ARG THR GLY VAL ALA SEQRES 31 A 665 GLY ILE ALA LYS ASN ARG GLY THR LEU HIS GLU ILE HIS SEQRES 32 A 665 LEU SER ASN LEU TYR ILE HIS ASP VAL GLU GLY ASN VAL SEQRES 33 A 665 TYR ASP LYS HIS MET ASN ASN GLY GLY ILE TYR PHE THR SEQRES 34 A 665 CYS LEU LYS PRO GLU ALA GLU GLU LYS THR GLY VAL ALA SEQRES 35 A 665 ARG TYR GLU ASN VAL SER VAL ARG GLY CYS HIS LEU LYS SEQRES 36 A 665 ARG THR SER ARG TRP GLY ILE ALA VAL GLY TYR SER TYR SEQRES 37 A 665 LYS CYS LYS GLU PHE MET THR ALA GLU LEU PRO ASP GLU SEQRES 38 A 665 LEU PHE GLU ARG TYR GLY HIS HIS ASN ILE TYR ILE ALA SEQRES 39 A 665 ASP ASN TYR VAL GLU GLU ILE GLY GLY ASP GLY ILE THR SEQRES 40 A 665 VAL MET TYR ALA MET LYS PRO LEU VAL GLU TYR ASN SER SEQRES 41 A 665 GLY ASP SER CYS ALA LEU GLU MET ASN ASP ARG TYR TYR SEQRES 42 A 665 THR GLU PRO GLU ASP ARG ALA GLY LYS VAL ALA ALA GLY SEQRES 43 A 665 ILE TRP PRO TRP LYS CYS LYS ASP ALA LEU LEU THR TYR SEQRES 44 A 665 ASN GLU MET ARG ASP MET ARG LEU ASN GLN ASP SER MET SEQRES 45 A 665 ALA TRP ASP ALA ASP SER GLY ASP GLY THR LEU TYR GLN SEQRES 46 A 665 TYR ASN TYR SER HIS LEU ASN GLU GLY GLY CYS VAL MET SEQRES 47 A 665 PHE CYS LEU GLU GLU ALA ILE HIS ASN GLU PHE ARG TYR SEQRES 48 A 665 ASN VAL SER VAL ASP ASP LEU GLY GLY LEU ILE SER PRO SEQRES 49 A 665 SER GLY ASN PRO ASP ALA TRP ILE HIS HIS ASN VAL PHE SEQRES 50 A 665 TYR ARG ARG ALA GLU VAL PRO PHE VAL ARG PRO HIS MET SEQRES 51 A 665 ASP ASP GLY LYS TYR VAL ALA GLU GLU ASN GLU ILE HIS SEQRES 52 A 665 LEU ILE HET NAG B 1 15 HET GAL B 2 11 HET PGE A 703 10 HET NA A 704 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM PGE TRIETHYLENE GLYCOL HETNAM NA SODIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 NAG C8 H15 N O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 PGE C6 H14 O4 FORMUL 4 NA NA 1+ FORMUL 5 HOH *706(H2 O) HELIX 1 AA1 ASN A 7 GLY A 22 1 16 HELIX 2 AA2 SER A 28 ALA A 47 1 20 HELIX 3 AA3 SER A 54 ASP A 60 5 7 HELIX 4 AA4 ASP A 61 ALA A 71 1 11 HELIX 5 AA5 ASN A 77 ASN A 83 1 7 HELIX 6 AA6 THR A 94 TYR A 113 1 20 HELIX 7 AA7 THR A 127 ASN A 138 1 12 HELIX 8 AA8 GLN A 139 PHE A 142 5 4 HELIX 9 AA9 SER A 151 ASN A 178 1 28 HELIX 10 AB1 ASN A 201 ARG A 223 1 23 HELIX 11 AB2 SER A 266 LEU A 273 1 8 HELIX 12 AB3 ALA A 433 GLY A 438 1 6 HELIX 13 AB4 LYS A 467 MET A 472 5 6 HELIX 14 AB5 PRO A 477 GLY A 485 1 9 SHEET 1 AA1 2 LEU A 117 VAL A 118 0 SHEET 2 AA1 2 HIS A 121 LYS A 122 -1 O HIS A 121 N VAL A 118 SHEET 1 AA213 CYS A 244 VAL A 247 0 SHEET 2 AA213 GLN A 280 GLU A 284 1 O LEU A 282 N TYR A 245 SHEET 3 AA213 ILE A 306 TYR A 311 1 O GLY A 309 N LEU A 283 SHEET 4 AA213 LEU A 358 GLU A 361 1 O GLU A 361 N ILE A 308 SHEET 5 AA213 THR A 396 SER A 403 1 O SER A 403 N VAL A 360 SHEET 6 AA213 ARG A 441 ARG A 448 1 O ARG A 441 N LEU A 397 SHEET 7 AA213 HIS A 487 ALA A 492 1 O TYR A 490 N VAL A 445 SHEET 8 AA213 LEU A 513 GLU A 515 1 O LEU A 513 N ILE A 491 SHEET 9 AA213 LEU A 554 THR A 556 1 O LEU A 554 N VAL A 514 SHEET 10 AA213 LEU A 581 GLN A 583 1 O LEU A 581 N LEU A 555 SHEET 11 AA213 GLU A 606 ARG A 608 1 O ARG A 608 N TYR A 582 SHEET 12 AA213 TRP A 629 HIS A 631 1 O TRP A 629 N PHE A 607 SHEET 13 AA213 VAL A 654 GLU A 656 1 O VAL A 654 N ILE A 630 SHEET 1 AA312 VAL A 288 GLU A 290 0 SHEET 2 AA312 LEU A 318 GLN A 320 1 O LEU A 318 N PHE A 289 SHEET 3 AA312 GLU A 364 ASN A 367 1 O GLU A 364 N ILE A 319 SHEET 4 AA312 TYR A 406 GLU A 411 1 O TYR A 406 N ILE A 365 SHEET 5 AA312 HIS A 451 SER A 456 1 O HIS A 451 N ILE A 407 SHEET 6 AA312 TYR A 495 GLU A 497 1 O TYR A 495 N LEU A 452 SHEET 7 AA312 SER A 518 ASP A 520 1 O SER A 518 N VAL A 496 SHEET 8 AA312 GLU A 559 ARG A 561 1 O ARG A 561 N GLY A 519 SHEET 9 AA312 TYR A 586 HIS A 588 1 O TYR A 586 N MET A 560 SHEET 10 AA312 VAL A 611 VAL A 613 1 O VAL A 613 N SER A 587 SHEET 11 AA312 VAL A 634 ARG A 637 1 O TYR A 636 N SER A 612 SHEET 12 AA312 GLU A 659 LEU A 662 1 O HIS A 661 N PHE A 635 SHEET 1 AA4 3 LEU A 294 LEU A 296 0 SHEET 2 AA4 3 ARG A 343 TYR A 353 1 O LEU A 351 N LEU A 294 SHEET 3 AA4 3 ILE A 326 ASP A 330 -1 N GLN A 329 O GLY A 344 SHEET 1 AA5 7 LEU A 294 LEU A 296 0 SHEET 2 AA5 7 ARG A 343 TYR A 353 1 O LEU A 351 N LEU A 294 SHEET 3 AA5 7 ASN A 383 ALA A 391 1 O ALA A 388 N VAL A 350 SHEET 4 AA5 7 GLY A 422 CYS A 428 1 O THR A 427 N GLY A 389 SHEET 5 AA5 7 TRP A 458 SER A 465 1 O GLY A 463 N PHE A 426 SHEET 6 AA5 7 ILE A 504 MET A 507 1 O MET A 507 N VAL A 462 SHEET 7 AA5 7 ILE A 545 TRP A 548 1 O TRP A 548 N VAL A 506 SHEET 1 AA6 3 TRP A 572 ALA A 574 0 SHEET 2 AA6 3 VAL A 595 CYS A 598 1 O MET A 596 N ALA A 574 SHEET 3 AA6 3 ILE A 620 SER A 623 1 O SER A 621 N VAL A 595 SHEET 1 AA7 2 GLY A 577 ASP A 578 0 SHEET 2 AA7 2 ALA A 602 ILE A 603 1 O ILE A 603 N GLY A 577 LINK O3 NAG B 1 C1 GAL B 2 1555 1555 1.43 LINK O ARG A 394 NA NA A 704 1555 1555 2.32 LINK O THR A 396 NA NA A 704 1555 1555 2.31 LINK NA NA A 704 O HOH A 879 1555 1555 2.21 LINK NA NA A 704 O HOH A1195 1555 1555 2.73 LINK NA NA A 704 O HOH A1326 1555 1555 2.44 CISPEP 1 SER A 456 ARG A 457 0 -2.75 CRYST1 132.295 132.295 82.200 90.00 90.00 120.00 P 31 2 1 6 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 0.007559 0.004364 0.000000 0.00000 SCALE2 0.000000 0.008728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012165 0.00000