HEADER STRUCTURAL GENOMICS 22-JUN-22 7Y7N TITLE CRYSTAL STRUCTURE OF DUF371 DOMAIN-CONTAINING PROTEIN FROM TITLE 2 METHANOBREVIBACTER RUMINANTIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOBREVIBACTER RUMINANTIUM; SOURCE 3 ORGANISM_TAXID: 634498; SOURCE 4 STRAIN: ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1; SOURCE 5 GENE: MRU_1462; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 561 KEYWDS UNKNOW FUNCTION, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR Q.YANG,Z.LAI REVDAT 2 29-NOV-23 7Y7N 1 REMARK REVDAT 1 12-JUL-23 7Y7N 0 JRNL AUTH Q.YANG,Z.LAI JRNL TITL CRYSTAL STRUCTURE OF DUF371 DOMAIN-CONTAINING PROTEIN FROM JRNL TITL 2 METHANOBREVIBACTER RUMINANTIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.876 REMARK 3 FREE R VALUE TEST SET COUNT : 781 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1094 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1076 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.01100 REMARK 3 B22 (A**2) : 1.01100 REMARK 3 B33 (A**2) : -2.02200 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): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.099 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1090 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1070 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1465 ; 1.729 ; 1.629 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2491 ; 1.412 ; 1.598 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 136 ; 7.390 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;31.028 ;25.102 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 220 ;14.188 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;10.934 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 152 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1187 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 203 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 168 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 22 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 529 ; 0.157 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 46 ; 0.149 ; 0.200 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): 547 ; 2.536 ; 2.987 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 546 ; 2.531 ; 2.987 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 682 ; 3.251 ; 4.472 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 683 ; 3.249 ; 4.472 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 543 ; 4.030 ; 3.504 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 543 ; 4.030 ; 3.504 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 783 ; 6.078 ; 5.037 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 784 ; 6.074 ; 5.036 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 : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7Y7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300029079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JAN-22 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) : 0.97919 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16164 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 44.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 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) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 1.59700 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: NULL REMARK 200 STARTING MODEL: 3CBN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.00% W/V POLYETHYLENE GLYCOL REMARK 280 8,000,5.00% W/V GLYCEROL,100 MM POTASSIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.93850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.67700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.67700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.96925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.67700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.67700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.90775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.67700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.67700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.96925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.67700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.67700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 101.90775 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 67.93850 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 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 251 LIES ON A SPECIAL POSITION. 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 HD1 HIS A 81 H ASP A 83 1.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Y7N A 1 137 UNP D3E451 D3E451_METRM 1 137 SEQRES 1 A 137 MET ASN PHE LYS ILE LYS ALA LYS GLY HIS LYS ASN VAL SEQRES 2 A 137 LEU SER LEU HIS LYS SER THR PHE GLU ILE THR LYS ASP SEQRES 3 A 137 LYS ASP LEU SER LEU SER GLY ASP CYS ILE ILE GLY LEU SEQRES 4 A 137 ASP ILE ASP LYS CYS MET LEU ASP PHE PRO LYS GLU PHE SEQRES 5 A 137 LYS GLU LYS LEU ALA ASN ASP GLU THR ILE VAL THR VAL SEQRES 6 A 137 LYS LEU LYS SER PRO ASN ALA TYR ASP GLU ILE VAL GLY SEQRES 7 A 137 TYR GLY HIS HIS ASP LEU THR LEU ASP HIS PRO THR ASP SEQRES 8 A 137 ILE VAL CYS ARG LYS SER ASP PHE ILE CYS SER ARG THR SEQRES 9 A 137 LEU MET ILE LYS SER ASP LYS ALA ALA ILE ASP LEU ASN SEQRES 10 A 137 ARG ASP LEU ILE GLU ASP LEU ALA ASN GLY GLU SER LEU SEQRES 11 A 137 ASP VAL GLU ILE ILE LEU SER FORMUL 2 HOH *52(H2 O) HELIX 1 AA1 CYS A 44 PHE A 48 5 5 HELIX 2 AA2 PRO A 49 ALA A 57 1 9 HELIX 3 AA3 ALA A 112 LEU A 116 5 5 HELIX 4 AA4 ASN A 117 ASN A 126 1 10 SHEET 1 AA1 4 ASN A 2 LYS A 8 0 SHEET 2 AA1 4 SER A 129 SER A 137 -1 O VAL A 132 N ILE A 5 SHEET 3 AA1 4 ILE A 62 LYS A 68 -1 N LYS A 68 O ASP A 131 SHEET 4 AA1 4 TYR A 73 TYR A 79 -1 O GLY A 78 N VAL A 63 SHEET 1 AA2 4 ILE A 36 GLY A 38 0 SHEET 2 AA2 4 THR A 20 THR A 24 1 N GLU A 22 O ILE A 37 SHEET 3 AA2 4 ASP A 91 ARG A 95 -1 O CYS A 94 N PHE A 21 SHEET 4 AA2 4 THR A 104 MET A 106 1 O LEU A 105 N VAL A 93 CRYST1 47.354 47.354 135.877 90.00 90.00 90.00 P 41 21 2 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 0.021118 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007360 0.00000