HEADER MOTOR PROTEIN 13-MAR-17 5NFD TITLE ANTIPARALLEL MONOMERIC COILED COIL OF KIF21A COMPND MOL_ID: 1; COMPND 2 MOLECULE: KINESIN-LIKE PROTEIN KIF21A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 938-1017; COMPND 5 SYNONYM: KINESIN-LIKE PROTEIN KIF2,RENAL CARCINOMA ANTIGEN NY-REN-62; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KIF21A, KIAA1708, KIF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COILED COIL, KINESIN, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.H.W.KRAATZ,S.BIANCHI,M.O.STEINMETZ REVDAT 3 03-OCT-18 5NFD 1 JRNL REVDAT 2 05-SEP-18 5NFD 1 JRNL REVDAT 1 02-MAY-18 5NFD 0 JRNL AUTH S.H.W.KRAATZ,S.BIANCHI,M.O.STEINMETZ JRNL TITL COMBINATORIAL USE OF DISULFIDE BRIDGES AND NATIVE SULFUR-SAD JRNL TITL 2 PHASING FOR RAPID STRUCTURE DETERMINATION OF COILED-COILS. JRNL REF BIOSCI. REP. V. 38 2018 JRNL REFN ISSN 1573-4935 JRNL PMID 30135143 JRNL DOI 10.1042/BSR20181073 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1965 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 8778 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1554 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 39.5042 - 4.8370 1.00 1457 155 0.2015 0.2378 REMARK 3 2 4.8370 - 3.8403 1.00 1445 167 0.1724 0.2012 REMARK 3 3 3.8403 - 3.3552 1.00 1466 156 0.1726 0.2119 REMARK 3 4 3.3552 - 3.0485 1.00 1479 163 0.2214 0.2528 REMARK 3 5 3.0485 - 2.8301 1.00 1429 158 0.2084 0.3024 REMARK 3 6 2.8301 - 2.6633 1.00 1484 167 0.2067 0.2593 REMARK 3 7 2.6633 - 2.5299 1.00 1465 169 0.2162 0.2491 REMARK 3 8 2.5299 - 2.4198 0.96 1391 149 0.2025 0.2453 REMARK 3 9 2.4198 - 2.3267 0.80 1158 136 0.2023 0.2668 REMARK 3 10 2.3267 - 2.2464 0.57 797 97 0.2216 0.2380 REMARK 3 11 2.2464 - 2.1762 0.21 314 37 0.2220 0.2196 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.250 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 : 0.002 1246 REMARK 3 ANGLE : 0.426 1657 REMARK 3 CHIRALITY : 0.025 185 REMARK 3 PLANARITY : 0.001 222 REMARK 3 DIHEDRAL : 10.764 525 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 5NFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003936. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-15 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.0664 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8779 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 41.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 54.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 35.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.07400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.0, 20% ISOPROPANOL, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 16.98500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.97500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.83500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.97500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.83500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ASN A 41 REMARK 465 GLY A 42 REMARK 465 GLU A 43 REMARK 465 GLY A 44 REMARK 465 ASP A 45 REMARK 465 ALA A 82 REMARK 465 LYS A 83 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 ALA B 82 REMARK 465 LYS B 83 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 ND2 ASN B 41 O HOH B 101 1.82 REMARK 500 O HOH B 129 O HOH B 155 2.01 REMARK 500 O HOH A 139 O HOH B 109 2.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 5NFD A 4 83 UNP Q7Z4S6 KI21A_HUMAN 938 1017 DBREF 5NFD B 4 83 UNP Q7Z4S6 KI21A_HUMAN 938 1017 SEQADV 5NFD GLY A 2 UNP Q7Z4S6 EXPRESSION TAG SEQADV 5NFD SER A 3 UNP Q7Z4S6 EXPRESSION TAG SEQADV 5NFD CYS A 13 UNP Q7Z4S6 MET 947 ENGINEERED MUTATION SEQADV 5NFD GLY B 2 UNP Q7Z4S6 EXPRESSION TAG SEQADV 5NFD SER B 3 UNP Q7Z4S6 EXPRESSION TAG SEQADV 5NFD CYS B 13 UNP Q7Z4S6 MET 947 ENGINEERED MUTATION SEQRES 1 A 82 GLY SER MET THR ILE SER ASN MET GLU ALA ASP CYS ASN SEQRES 2 A 82 ARG LEU LEU LYS GLN ARG GLU GLU LEU THR LYS ARG ARG SEQRES 3 A 82 GLU LYS LEU SER LYS ARG ARG GLU LYS ILE VAL LYS GLU SEQRES 4 A 82 ASN GLY GLU GLY ASP LYS ASN VAL ALA ASN ILE ASN GLU SEQRES 5 A 82 GLU MET GLU SER LEU THR ALA ASN ILE ASP TYR ILE ASN SEQRES 6 A 82 ASP SER ILE SER ASP CYS GLN ALA ASN ILE MET GLN MET SEQRES 7 A 82 GLU GLU ALA LYS SEQRES 1 B 82 GLY SER MET THR ILE SER ASN MET GLU ALA ASP CYS ASN SEQRES 2 B 82 ARG LEU LEU LYS GLN ARG GLU GLU LEU THR LYS ARG ARG SEQRES 3 B 82 GLU LYS LEU SER LYS ARG ARG GLU LYS ILE VAL LYS GLU SEQRES 4 B 82 ASN GLY GLU GLY ASP LYS ASN VAL ALA ASN ILE ASN GLU SEQRES 5 B 82 GLU MET GLU SER LEU THR ALA ASN ILE ASP TYR ILE ASN SEQRES 6 B 82 ASP SER ILE SER ASP CYS GLN ALA ASN ILE MET GLN MET SEQRES 7 B 82 GLU GLU ALA LYS FORMUL 3 HOH *100(H2 O) HELIX 1 AA1 MET A 4 GLU A 40 1 37 HELIX 2 AA2 ASN A 47 GLU A 81 1 35 HELIX 3 AA3 THR B 5 GLY B 42 1 38 HELIX 4 AA4 LYS B 46 GLU B 81 1 36 SSBOND 1 CYS A 13 CYS A 72 1555 1555 2.03 SSBOND 2 CYS B 13 CYS B 72 1555 1555 2.03 CRYST1 33.970 41.670 123.950 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 0.029438 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023998 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008068 0.00000