PDB Short entry for 6IGW HEADER MEMBRANE PROTEIN 26-SEP-18 6IGW TITLE MPZL1 MUTANT - S86G, V145G, Q146K,P147T,G148S COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN PROTEIN ZERO-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 36-162; COMPND 5 SYNONYM: PROTEIN ZERO-RELATED; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MPZL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RECEPTOR, GLYCOPROTEIN, TRANSMEMBRANE, IMMUNOGLOBULIN, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.YU REVDAT 3 22-NOV-23 6IGW 1 REMARK REVDAT 2 05-DEC-18 6IGW 1 JRNL REVDAT 1 28-NOV-18 6IGW 0 JRNL AUTH T.YU,L.LIANG,X.ZHAO,Y.YIN JRNL TITL STRUCTURAL AND BIOCHEMICAL STUDIES OF THE EXTRACELLULAR JRNL TITL 2 DOMAIN OF MYELIN PROTEIN ZERO-LIKE PROTEIN 1 JRNL REF BIOCHEM. BIOPHYS. RES. V. 506 883 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 30392906 JRNL DOI 10.1016/J.BBRC.2018.10.161 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 10880 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 541 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 36.9610 - 3.1415 0.99 2957 166 0.2156 0.2063 REMARK 3 2 3.1415 - 2.4937 1.00 2786 140 0.2575 0.2864 REMARK 3 3 2.4937 - 2.1785 1.00 2717 146 0.2759 0.2997 REMARK 3 4 2.1785 - 1.9793 0.69 1879 89 0.2805 0.3289 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.600 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 : 0.011 965 REMARK 3 ANGLE : 1.209 1307 REMARK 3 CHIRALITY : 0.095 141 REMARK 3 PLANARITY : 0.016 167 REMARK 3 DIHEDRAL : 22.715 346 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 6IGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-17 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.979 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: 3OAI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS-HCL PH 8.5, 1M LI2SO4, REMARK 280 1.8%(W/V) PEG8000, VAPOR DIFFUSION, TEMPERATURE 293K 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 96.68500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.99550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.99550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.34250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.99550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.99550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 145.02750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.99550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.99550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.34250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.99550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.99550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 145.02750 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 96.68500 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 SER A 36 REMARK 465 ALA A 37 REMARK 465 SER A 64 REMARK 465 THR A 65 REMARK 465 ASN A 159 REMARK 465 LEU A 160 REMARK 465 PRO A 161 REMARK 465 VAL A 162 REMARK 465 LEU A 163 REMARK 465 GLU A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 PRO A 140 C - N - CD ANGL. DEV. = -15.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 6IGW A 36 162 UNP O95297 MPZL1_HUMAN 36 162 SEQADV 6IGW GLY A 86 UNP O95297 SER 86 ENGINEERED MUTATION SEQADV 6IGW GLY A 145 UNP O95297 VAL 145 ENGINEERED MUTATION SEQADV 6IGW LYS A 146 UNP O95297 GLN 146 ENGINEERED MUTATION SEQADV 6IGW THR A 147 UNP O95297 PRO 147 ENGINEERED MUTATION SEQADV 6IGW SER A 148 UNP O95297 GLY 148 ENGINEERED MUTATION SEQADV 6IGW LEU A 163 UNP O95297 EXPRESSION TAG SEQADV 6IGW GLU A 164 UNP O95297 EXPRESSION TAG SEQADV 6IGW HIS A 165 UNP O95297 EXPRESSION TAG SEQADV 6IGW HIS A 166 UNP O95297 EXPRESSION TAG SEQADV 6IGW HIS A 167 UNP O95297 EXPRESSION TAG SEQADV 6IGW HIS A 168 UNP O95297 EXPRESSION TAG SEQADV 6IGW HIS A 169 UNP O95297 EXPRESSION TAG SEQADV 6IGW HIS A 170 UNP O95297 EXPRESSION TAG SEQRES 1 A 135 SER ALA LEU GLU VAL TYR THR PRO LYS GLU ILE PHE VAL SEQRES 2 A 135 ALA ASN GLY THR GLN GLY LYS LEU THR CYS LYS PHE LYS SEQRES 3 A 135 SER THR SER THR THR GLY GLY LEU THR SER VAL SER TRP SEQRES 4 A 135 SER PHE GLN PRO GLU GLY ALA ASP THR THR VAL GLY PHE SEQRES 5 A 135 PHE HIS TYR SER GLN GLY GLN VAL TYR LEU GLY ASN TYR SEQRES 6 A 135 PRO PRO PHE LYS ASP ARG ILE SER TRP ALA GLY ASP LEU SEQRES 7 A 135 ASP LYS LYS ASP ALA SER ILE ASN ILE GLU ASN MET GLN SEQRES 8 A 135 PHE ILE HIS ASN GLY THR TYR ILE CYS ASP VAL LYS ASN SEQRES 9 A 135 PRO PRO ASP ILE VAL GLY LYS THR SER HIS ILE ARG LEU SEQRES 10 A 135 TYR VAL VAL GLU LYS GLU ASN LEU PRO VAL LEU GLU HIS SEQRES 11 A 135 HIS HIS HIS HIS HIS FORMUL 2 HOH *44(H2 O) HELIX 1 AA1 TYR A 100 LYS A 104 5 5 HELIX 2 AA2 ASP A 112 LYS A 116 5 5 HELIX 3 AA3 GLN A 126 HIS A 129 5 4 SHEET 1 AA1 2 GLU A 39 TYR A 41 0 SHEET 2 AA1 2 LYS A 59 LYS A 61 -1 O LYS A 59 N TYR A 41 SHEET 1 AA2 6 GLU A 45 ALA A 49 0 SHEET 2 AA2 6 LYS A 146 VAL A 155 1 O VAL A 155 N VAL A 48 SHEET 3 AA2 6 GLY A 131 LYS A 138 -1 N TYR A 133 O ILE A 150 SHEET 4 AA2 6 SER A 71 PRO A 78 -1 N SER A 73 O ASP A 136 SHEET 5 AA2 6 VAL A 85 SER A 91 -1 O VAL A 85 N PHE A 76 SHEET 6 AA2 6 GLN A 94 LEU A 97 -1 O TYR A 96 N HIS A 89 SHEET 1 AA3 3 GLY A 54 LEU A 56 0 SHEET 2 AA3 3 ILE A 120 ILE A 122 -1 O ILE A 122 N GLY A 54 SHEET 3 AA3 3 ILE A 107 TRP A 109 -1 N SER A 108 O ASN A 121 CISPEP 1 PRO A 140 PRO A 141 0 3.33 CRYST1 39.991 39.991 193.370 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 0.025006 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005171 0.00000