HEADER CYTOSOLIC PROTEIN 03-SEP-18 6HJH TITLE MYXOCOCCUS XANTHUS MGLA BOUND TO GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUTUAL GLIDING-MOTILITY PROTEIN MGLA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYXOCOCCUS XANTHUS; SOURCE 3 ORGANISM_TAXID: 34; SOURCE 4 GENE: MGLA, MXAN_1925; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL GTPASE, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.F.VARELA,J.CHERFILS REVDAT 2 17-JAN-24 6HJH 1 REMARK REVDAT 1 04-DEC-19 6HJH 0 JRNL AUTH C.GALICIA,S.LHOSPICE,P.F.VARELA,S.TRAPANI,W.ZHANG,J.NAVAZA, JRNL AUTH 2 J.HERROU,T.MIGNOT,J.CHERFILS JRNL TITL MGLA FUNCTIONS AS A THREE-STATE GTPASE TO CONTROL MOVEMENT JRNL TITL 2 REVERSALS OF MYXOCOCCUS XANTHUS. JRNL REF NAT COMMUN V. 10 5300 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31757955 JRNL DOI 10.1038/S41467-019-13274-3 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 46.6 REMARK 3 NUMBER OF REFLECTIONS : 2264 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 : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.316 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 112 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.69 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 37.73 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 512 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2670 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 488 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.69 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1519 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 90.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 103.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.39350 REMARK 3 B22 (A**2) : 2.39350 REMARK 3 B33 (A**2) : -4.78700 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.420 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 1.104 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.789 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1577 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2139 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 560 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 39 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 237 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1577 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 207 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1768 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.10 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 23.16 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|3 - A|192 } REMARK 3 ORIGIN FOR THE GROUP (A): 40.1012 -10.3245 1.8733 REMARK 3 T TENSOR REMARK 3 T11: 0.1427 T22: -0.2096 REMARK 3 T33: -0.1170 T12: -0.0164 REMARK 3 T13: -0.1044 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 3.7278 L22: 3.7529 REMARK 3 L33: 8.7741 L12: -0.6349 REMARK 3 L13: 0.0845 L23: 1.8815 REMARK 3 S TENSOR REMARK 3 S11: 0.0337 S12: 0.2959 S13: -0.0177 REMARK 3 S21: -0.1680 S22: -0.0368 S23: -0.2244 REMARK 3 S31: -0.1534 S32: 0.1335 S33: 0.0031 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200011764. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4841 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 47.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.23000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 1.60000 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: MOLREP REMARK 200 STARTING MODEL: 3T1O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES 0.1M, PEG 4000 30%, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 64.72667 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 32.36333 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 32.36333 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 64.72667 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: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 1 REMARK 465 SER A 2 REMARK 465 LYS A 193 REMARK 465 GLY A 194 REMARK 465 GLY A 195 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 6 -88.39 47.32 REMARK 500 LEU A 22 85.73 64.01 REMARK 500 CYS A 23 -41.56 -133.99 REMARK 500 ILE A 32 -83.06 -69.24 REMARK 500 THR A 36 -136.99 -145.46 REMARK 500 THR A 40 -50.97 -168.11 REMARK 500 THR A 51 -60.36 -98.49 REMARK 500 SER A 63 -32.31 -152.78 REMARK 500 PRO A 135 119.58 -35.60 REMARK 500 ARG A 161 59.21 -119.19 REMARK 500 ILE A 163 127.22 82.10 REMARK 500 LEU A 191 13.36 -150.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 200 DBREF 6HJH A 1 195 UNP Q1DB04 MGLA_MYXXD 1 195 SEQRES 1 A 195 MET SER PHE ILE ASN TYR SER SER ARG GLU ILE ASN CYS SEQRES 2 A 195 LYS ILE VAL TYR TYR GLY PRO GLY LEU CYS GLY LYS THR SEQRES 3 A 195 THR ASN LEU GLN TYR ILE TYR ASN LYS THR ALA ALA GLU SEQRES 4 A 195 THR LYS GLY LYS LEU ILE SER LEU SER THR GLU THR ASP SEQRES 5 A 195 ARG THR LEU PHE PHE ASP PHE LEU PRO LEU SER LEU GLY SEQRES 6 A 195 GLU ILE ARG GLY PHE LYS THR ARG PHE HIS LEU TYR THR SEQRES 7 A 195 VAL PRO GLY GLN VAL PHE TYR ASP ALA SER ARG LYS LEU SEQRES 8 A 195 ILE LEU LYS GLY VAL ASP GLY VAL VAL PHE VAL ALA ASP SEQRES 9 A 195 SER GLN ILE GLU ARG MET GLU ALA ASN MET GLU SER LEU SEQRES 10 A 195 GLU ASN LEU ARG ILE ASN LEU ALA GLU GLN GLY TYR ASP SEQRES 11 A 195 LEU ASN LYS ILE PRO TYR VAL ILE GLN TYR ASN LYS ARG SEQRES 12 A 195 ASP LEU PRO ASN ALA VAL THR VAL GLU GLU MET ARG LYS SEQRES 13 A 195 ALA LEU ASN HIS ARG ASN ILE PRO GLU TYR GLN ALA VAL SEQRES 14 A 195 ALA PRO THR GLY VAL GLY VAL PHE ASP THR LEU LYS ALA SEQRES 15 A 195 VAL ALA LYS LEU VAL LEU THR GLU LEU LYS LYS GLY GLY HET GDP A 200 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 HOH *(H2 O) HELIX 1 AA1 ASN A 5 ARG A 9 5 5 HELIX 2 AA2 GLY A 24 ASN A 34 1 11 HELIX 3 AA3 LYS A 90 LYS A 94 5 5 HELIX 4 AA4 MET A 110 LEU A 124 1 15 HELIX 5 AA5 THR A 150 LEU A 158 1 9 HELIX 6 AA6 VAL A 176 GLU A 190 1 15 SHEET 1 AA1 7 ILE A 45 SER A 48 0 SHEET 2 AA1 7 ARG A 53 ASP A 58 -1 O THR A 54 N LEU A 47 SHEET 3 AA1 7 HIS A 75 THR A 78 -1 O LEU A 76 N PHE A 57 SHEET 4 AA1 7 ILE A 15 TYR A 18 1 N ILE A 15 O HIS A 75 SHEET 5 AA1 7 GLY A 98 ASP A 104 1 O VAL A 100 N TYR A 18 SHEET 6 AA1 7 TYR A 136 ASN A 141 1 O GLN A 139 N PHE A 101 SHEET 7 AA1 7 GLU A 165 GLN A 167 1 O TYR A 166 N TYR A 140 CISPEP 1 ASN A 162 ILE A 163 0 -1.28 SITE 1 AC1 15 LEU A 22 CYS A 23 GLY A 24 LYS A 25 SITE 2 AC1 15 THR A 26 THR A 27 PRO A 80 GLY A 81 SITE 3 AC1 15 ASN A 141 LYS A 142 ASP A 144 LEU A 145 SITE 4 AC1 15 VAL A 169 ALA A 170 PRO A 171 CRYST1 73.550 73.550 97.090 90.00 90.00 120.00 P 32 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 0.013596 0.007850 0.000000 0.00000 SCALE2 0.000000 0.015700 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010300 0.00000